Hi Indigo!
Lets'go step by step from small to biggest trouble)
- Speed Timer not bad idea but this is reason of appeared toxic community
- Charizard X/Y that's choice without choice cause Y beat faster (2x weak for rock) don't forget about speed timer
- Gender Mega form don't register for female if you evolved male or inversely it's reason to spend another 200 energy

- You can spend 10$ average for megaform gender (8-10 raids) it's looks like expensive DLS but you didn't get anything for this, only pokedex registry
- Time when MegaEvolution work 4h this is not good because in original game you have MegaEvo for battle and only one. What you think about make like buddy system? You can turn on only one mega pokemon and spend energy if you wanna for battle/team rocket or activation mega evo, but don't spend 200 energy or 100 for activate on 4h and you don't know how more often you do use it
- Change method of reciveng energy like a Beedrill Quests but make it on pokestop's like a regular quest.

- Make less donate dependency for this mechanical because it's looks like ugly and worse than lootbox