Looking of all 3 of fenix’s prestiges they are mostly only upsides. P1 instead of a hero unit you have 2.5 call downs to trivialize most wave configurations. P2 and P3 Focus on champion buffing, but which does it better, because P3 might as well be a straight upgrade, champs refund 75% when they die and you still have all 3 fenix suits to use in the army, all of the cost of champions dying more offten, wait you want thta because avenging Protocall is also buffed. Meanwhile P2 is about hyper buffing the champs, Kaldalis kills all ground units and tali’s does the same to mutas, with mojo dealing with anything else in the air, while colarian tanks and war bringer nukes the highest priority target (every 5 second) with taldarin acting as cleanup if Kaldalis dies. With upside of half off units to better ramp up hyper champs, and discouraging using your army to fight because half hp and atk, which is the play style anyways. To a certain extent because of how they were designed all are pretty much upgrades compared to P0, transmutation is the only 1 I’d think P0 would be better then P3. But when it comes down to it, which is better P2 or P3. Exchange the army for hero’s, or exchange the hero’s for better hero’s. I think P3 gives up less,but as I’ve yet to play with P3, does P2 just give more?
“Edit was to fix some spelling”
I don’t know if I would consider either to be straight upgrades (P2 discourages using Fenix’s army entirely and P3 means solo champions are not as stat-efficient they are under P0), but if you don’t notice the drawbacks while playing them, I’d guess they gel with your playstyle nicely, which is great 
Having levelled both but not yet played them with full masteries, I’d say P2 is the more thematically exciting, and the one I’m more excited to fully play. It essentially turns Fenix into a Protoss Tychus, and using fewer, stronger units to fight is a refreshing change on the commander. You’re still going to need to macro your butt off, though
P3 I find encourages single- or double-unit comps. Normally the play on P0 Fenix is to rush out 4-6 champions early-game and build your comp from there; with P3, since your champions don’t get extra shields or HP, you’re not rewarded as much for rushing them out but rather focusing on a couple of unit types to take full advantage of both P3 and Tactical Data Web. It arguably simplifies Fenix’s macro since you’re more incentivized to play with a mass of a couple unit types.
Once I finish prestiging everyone, I’ll be most excited to try out Fenix’s talents at their full potential.
P2 is better but in the sense that it buffs the Fenix’s strongest composition. P3 is more flexibility for less buff.
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IF they need Balancing (not sure that they do)
I’d remove Tactical Data Web from P3 (to make it even more suited to allow the “mass one unit” strategy as opposed to 6 champion)
Maybe increase champion cost for P2 (since the units are cheap)
For P1, fix the arbiter bug that lets it be resummoned every 20 seconds
I would definitely take Fenix’s P3 over his P2. His army is significantly weaker with his P3 whereas only his champions would take a hit. I’m ok with that since enhances his Avenging Protocol upgrade that much better.
With his P2 though, gateway focused armies are pretty bad. You need do Robo/Stargate armies instead and focus on armor/plasma shield upgrades. You should be able to afford all of this since your units are cheaper by 50% so there shouldn’t be a problem.
P2 is better played as a 6 champion army, sort of like Tychus, keeping the rest of the army out of combat but close-by so the champions can quickly transfer shells and re-engage combat. It’s simply not worth having fragile non-champion units in combat.
This way you can also skip armor upgrades and do very well with P2, because of Avenging Protocol and cheap replacement shells. Besides, a lot of the damage an army takes is from spell damage, which completely bypasses armor upgrades.
The one thing P3 has going for it is that you can F2 A-move, whereas P2 is not F2 friendly. You need to keep your champions on a dedicated hotkey from your army.
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That’s another way to look at his P2. I guess I prefer weaker heroes than a weaker army.
P2 prob if you separate champions from army
but I like P3, go immortal heavy with some scout support = machine gunning Immortal
The thing is P3 is another one of those mechanic that requires you to “lose something” then “gain benefit”. Fenix is more forgiving in this department but you honestly lose less and less as the game goes on. And frankly, if you’re micro’ing properly you’re not losing much.
I like the idea of P3 that it tries to buff in a different way but it is honestly a lose-lose benefit.
While P2’s army is definitely weaker, you’re not really getting them en mass. You need 20 supply to gain full benefit. That’s very little “extra army” to keep around. Conservator is your friend - get it, use it, shield army with it. Army is weaker but not “they touched me so I die” weak. 3-4 of each unit type is plenty to get the benefit, synergize, and keep each other alive.
I don’t agree (and I’ve seen this many times) of people keeping them far too separate. Yes, don’t rush head in with 6-7 zealots, group up your Champions and attack, then move your army. They are there for a reason 
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I prefer p2 because of how ridiculously strong champions become. Try maxing out kaldalis as fast as possible and then set him loose upon the map, it’s fun
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I did not enjoy leveling with P2 enabled at all cause all of my “shells” got killed by everything in just a few shots. Tactical Data Web benefits are meh at best. Does not buff Champion base stats, and Champions can easily get overwhelmed. I tried a bit after reaching lv15 but it is still not that impressive.
P3 is a straight eco upgrade and I like it, as your entire army theoretically only cost 25% of its original cost, meaning I can field more in the long run, and makes me feel Fenix being a “Protoss” rather than debuff-ed Zerg.
Just strip away additional synergy. For example, Immortal Adept Scout was a good deathball army; now I have no Adepts and Taldarin is machine gunning away
No conservator spam either
Currently rolling 3 Robo 4 Nexus 1 Stargate for vanilla Brut P3
P2 is 6 champions as other posters have said sort of Tychus style.
P3 is where you go immortal / scout, adept / scout, mass adepts; plus you can do the 1 legionaire Kaldaris strat, warp a legionaire just before you fight or when Kaldaris dies so you keep the avenging protocol stack.
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please do not fight with the shells while running p2, they’re only there to max out TDW and be champion respawn points. the TDW benefits are pretty great but where it benefits the best is on kaldalis, as empowered blades affects his primary target; thus, TDW directly scales his attack damage. simply hotkey your champions and attack with only them and they will wreck everything.
which would only happen if you attack with only champions, which is what p2 encourages you to do? and p2 benefits champions far more than p3. p3 is really only useful on certain mutations i.e black death or double-edged where you know your champions are gonna die, so you capitalize on the refunds. plus there’s a whole ton of attack animation caps on certain champions that prevents them from reaching their theoretical dps (kaldalis included funnily enough), so the extra AP is very limited.
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If you know more, could you elaborate on these attack animation caps? Are they bugs, and how much do they affect the other champions?
basically, past a certain point, some champions simply cannot execute their attack animation any faster, and thus their attack speed gets hardcapped by this. warbringer is a standout example as even a few stacks of normal AP caps it hard. kaldalis is also suspect because of how it limits his potential with p3. taldarin, mojo, and talis are pretty fine tho, and clolarion is pretty much unaffected by AP anyway
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Poor Colarian, honnestly gets the short end of the stick, TDW buffs interdictions, which are of questionable usefulness, and AP is kinda not worth it on him, as losing a carrier sucks, because cost and build times. TDW buffing the lazer would be a buff, but I mean he is essentially the hull of 2 carriers ducktaped to a void ray, so not surprising.
Colarian needs a buff, particularly against air. I don’t think Fenix in general needs a buff. So I’d settle for some trade off (maybe a slight Kaldaris nerf) but Colarian needs some love.
Fenix champions kind of wreck ground comps but are so so against air, at least when it comes to his champions. So I think the solar beam if anything is what needs buffed.
To be fair what Fenix needs is mostly a BC killer, as Tali’s does scary things to muta clouds. But sky terran tends to sent as many BCs as Mutas, and tempast carrier forces are just as annoying. So Mojo warbringer nuking the T3 capital ships 1 at a time is kinda so slow. So even if solar beam is buffed it’d be dubious at best unless it starts acting like P1 swann drill, or Alarak destroyers.
Just spam Scouts. They are cheap, Fenix Stargates are cheap, and are recruited quickly