Zenyatta has a lot a problems have either been a problem since launch or have recently brought to light with the introduction of new abilities and characters.
Everything I state in this post should be considered.
I will go over each problem with him at the moment and what changes should be implemented.
General Changes
Secondary Fire
Currently: Consumes ammo before shots are fired and when shots are cancelled with Melee.
Change: Secondary fire no longer consumes ammo while charging. Now consumes ammo after being released.
Reason: So many times will you be charging up a secondary Fire shot just for you to have to cancel it and use your discord or harmony orb, this change would allow him to keep his ammo up and not have to worry about having to reload.
Reload
Currently: You cannot reload and use discord and harmony orb.
Change: Zenyatta can now reload and apply Discord and Harmony orb on target simultaneously.
Reason: This helps Zenyattas pace and allows for more control of his abilities.
Buffs and Changes
Harmony
Currently: Heals for 30hps
Change: Heals for 35hps
Reason: This change would allow for Zenyatta to give a better healing output to keep up with other healers.
Primary Damage
Currently: Deals 48 damage.
Change: Deals 48.2 damage.
Reason: 48 damage against 250 health heroes is very inconsistent, when discord is used against a 250 health hero, if Zenyatta were to hit 2 headshots he would deal a total of 249.6 damage.
This means that they would be left with .4 health.
(Yes you can have a decimal point as health but the game rounds it up visually as 1 health) This change would keep his consistency.
Hurtbox
Currently: It looks like this right now: KarQ Video on Hitboxes - skip to 13:42 to see Zenyatta hitbox
Change: Bring his hitbox down to reasonable size, and also give gaps in-between his hands/arms and legs; or lower his head hitbox size to be more in line with how it actually is.
Reason: He can easily take unnecessary damage and get destroyed by spread damage heroes.
Movement
Currently: All characters walk/move backwards at a slower pace.
Change: Zenyatta should be allowed to move in all directions at the same speed.
Reason: It will help with his movement issues and allow for better defensive play while keeping an eye on his target.
These are the things I think will help Zenyatta play Zenyatta better, it will help him survive a bit longer, and keep him up along with other supports.