A few things of note. First when replacing a skill not being able to see what skill your replacing is super annoying, it means I have to remember what the skill that is that slot is based on an icon on top of remembering what the skill dose and what synergies it uses, I'm sure this isnt intentional and will be delt with in your next update. Second the boss that jumps around if you kill him in the air his exp orb stays in the air making it unable to be collected, as well surely not intentional for higher pickup range to simply fix later on, my guess you will be adjusting fall, ground, collision, and hit box mechanics later on. Lastly I will say a 3 team survivors game usualy falls under the by team member active and passive upgrade per level. I take it your attempting to move away from it to a more broader spectrum of upgrades. GL with that, it creates more issues then you will care to fix. Doing it by team member by single skill per upgrade will allow far more balance. A broader spectrum upgrades will simply make certain skills super weak over time and certain skills game breakingly OP. Thus making it only one way to play to win, enjoy the mad complaints on that front. (Btw I'm just speculating this is the way you intend to go, if it's not ignore me. Its cool.)
Anyhow my suggestion is acually having each team member level separately on top of a team overall level. Each individual level of each team member simply giving fixed by level attributes (damage, range, speed, amount, area, ect). Then for overall team level per accumulated amount of levels total of individual levels get your skills (active/passive) and synergies. Thoughts on that is 3 active skill slots per team member and 1-3 passive skill slots per team member. As well as 1-2 combined active skill for team as well as 1-2 combined passive for the team. I suggest this becuase it leaves room for the broader spectrum upgrades while still leaving the by team member per level upgrades well enough that balancing is easy for the developer as just adjusting a single skill wont effect other skills in the process.
That said, super fan of roguelike survivors games, looking forward to seeing how this one turns out.