(Note: The info in this thread took hundreds of hours of questing, observation, and research, So I really hope it can be of some use in improving the service 
)
After several faction changes of my character over the last 10 months, I have noticed various oddities and issues, most are so minor as to likely never be worth the dev time to change, however there are some that are fairly major, and really something that should be fixed, especially being part of a paid service, only major things are noted here.
The largest problem is quests that reset every single time you faction change, and appear to be a single direction problem, some of these questchains ive completed 3 times on my character, which is getting pretty old
Losses going from Horde to Alliance (completed on alliance before swapping to horde, but gone upon rejoining the alliance)
Outland:
-WANTED: Zorbo the Advisor (ID 9940)
-Daggerfen Daviance (ID 10115)
-Torch Tossing (ID 11731)
-Torch Catching (ID 11657)
-Help for Mudsprocket (ID 11211)
Wotlk:
-My Old Enemy (ID 12464)
-Sharing A Bountiful Feast (ID 14064)
-Find Kurun! (ID 11981)
Cataclsym:
Agamaggan (ID 26906)
Take Them Down! (ID 26907)
Agamaggan’s Charge (ID 26905)
Going, Going, Guano! (ID 26901)
Into the Woods (ID 27683)
Visitors (ID 27684)
Taerar’s Fall (ID 25379)
Friends on The Other Side (ID 27469)
The Mind’s Eye (ID 26781)
Nothing a Couple of Melons Won’t Fix (ID 14193)
To the Hilt! (ID 14357)
Ten pounds of flesh (ID 14358)
Ongo’longo’s Revenge (ID 26515)
Venomous Secrets (ID 26525)
Summit of Fate (ID 26517)
Hunt the Keeper (ID 26526)
Enemy at our Roots (ID 28382)
Sasquatch Sighting (ID 25433)
Taming The Tamers (ID 25434)
Spiteful Sisters (ID 25436)
Ysondre’s Call (ID 25437)
Stinglasher (ID 25431)
Zukk’ash Infestation (ID 25429)
Ysondre’s Farewell (ID 25438)
Paving the Way (ID 28107) (And every quest in the twilight highlands storyline after this quest, totaling 44 quests both neutral and alliance)
MoP:
In the House of the Red Crane (ID 30273)
WoD:
Disrupting the Flow (ID 33917)
The Road to Kun-Lai (ID 38936)
Looking for Help (ID 34194)
Moonshell Claws (ID 36199)
Proving Your Worth (ID 36201)
Anglin’ In Our Garrison (ID 36202)
BFA:
Beneath the Waves (ID 48026)
Word from the Deep (ID 51538)
Losses going from Alliance to Horde (completed on Horde before swapping to Alliance, but gone upon rejoining the Horde)
BC:
Arrival in Outland (ID 10120)
Wotlk:
Scouting the sinkholes (ID 11684)
Sharing the Bounty (ID 14065)
Cata:
Favored Skull (ID 26323)
A Nose for this sort of thing (ID 26325)
Venture Mining Company (ID 26403)
There’s Someboy out there who wants it (ID 26493)
Akiris by the bundle (ID 26487)
It’s You!! (ID 26489)
Who’s a big troll? (ID 26330)
If they’re Just going to leave them lying around… (ID 26450)
Chabal (ID 26495)
Backdoor Dealings (ID 26550)
The Mosh’Ogg Bounty (ID 26399)
Eliminate the outcast (ID 26551)
Through the troll hole (ID 26552)
High Preistess Jeklik (ID 26553)
Plunging Into Zul’gurub (ID 26554)
High Preist Venoxis (ID 26555)
The Rise of the darkspear (ID 24607) (Plus other class ID’s)
The Basics: Hitting Things (ID 24639) (Plus other class ID’s)
Sharing The Land (ID 14438)
WoD:
Disrupt the Rituals (ID 35083)
Silence the Call (ID 35084)
Through the Nether (ID 35085)
The Void March (ID 35086)
The Nether Approaches (ID 35087)
The Shadow of the Void (ID 35088)
Super Seeds (ID 35406)
BFA:
Blood In the Tides (ID 53439)
Precious Metals (ID 53461)
All Wrapped Up (ID 53462)
Shadowlands:
Silent Vigil (ID 66170)
Assemble the Forsaken (ID 65657)
The Blight Congress (ID 65659)
Walk of Faith (ID 65660)
Consulting Our Allies (ID 65661)
House of Plagues (ID 65662)
Feed the Eater (ID 65663)
Essence of Plague (ID 65664)
Embodiment (ID 65665)
Return to Brill (ID 65666)
The Remedy of Lordaeron (ID 65667)
The Desolate Council (ID 65668)
Path of the Dark Rangers (ID 66091)
A Walk with Ghosts (ID 65788)
Faction change bugs:
Horde:
Murkblood Invasion Plans (Item ID 24558) (Item wont drop if you completed the Alliance version of the quest it starts)
Enchanted Highmaul Bracer (Item ID 115008) (Item wont drop if you completed the Alliance version)
Quel’Delar: Players who completed the questchain on Alliiance get stuck on Return to Myralion Sunblaze (ID 24558), the quest is not offered, Ive been told the followup fails to be offered as well if you get GM help with return to myralion,
Of Wolves and warriors (ID 34402) Quest is never offered to faction changed characters, attempting to share it lists “does not meet pre reqs”
We Need Each Other (ID 52131) Quest is never offered to faction changed characters.
Neutral:
Looking for Help (ID 34194/34758) (Quests are impossible to start on either faction after losing credit after faction changing at all, May be a problem for the whole 4 quest chain, unable to confirm)
The Way of the Tushui (ID 29414) (Faction changed Pandaren who go to the wandering isle are incapable of completing this quest due to the 60 second time limit on the isle, this quest requires 90 seconds of mediation)
Loss of credit:
Each time you faction change, some quests get reset intentionally, specifically neutral quests that are part of both an alliance and a horde questchain, Once you complete the neutral quest on both factions, you will always keep it on faction change (aside from ones mentioned above as being broken and get reset repeatedly)
However there also seems to be some cleanup thats being done that after reading the effects list, I think was meant to be removed,
After looking at an old copy of the faction change effects page it used to say
" * Faction-specific completed quests will be lost and will no longer count toward any completed quests counters"
This is no longer listed as an effect, but about 75% of the other factions quests are still being removed.
General Feedback: if these things got fixed, and 75% of faction specific quests stopped being cleared from your completion list after multiple faction changes, most collectors are scared of using the faction change service due to the risk of losing quests,
That part of faction changing was designed when quests were considered less of a collectable, Im honestly not sure if its still intended to be active to be honest considering its not even listed as an effect anymore,