I will say, I think this is probably the best balanced upgrade/combat system in one of TS' games so far. Though that does also come with it having harder limits than the others.
I definitely see what the start of the game meant with "You should prioritize one or two stats at most at least for now", since you definitely get more bang for your buck by trying to go deep in a skill tree than spreading things out, but also each play style has it's own unique balance between offence and defense options. Alchemy/Cunning having a lot more DOT, utility and evasion chance, Might/Phys giving extra health for defense and trying to sort of play high risk, high reward by pretty much using your HP as ammo, and Esper/Wit giving a fairly balanced style with flat damage negation with barrier, and lust powered attacks later in the skill tree.
I will say though, Esper does kind of seem better in terms of combat than Alchemy, even though Alchemy has a lot of different statuses that can be applied, utility, and so on, it kind of suffers for a lack of damage, so I've kind of had to hard pivot my build from being alchemy/esper with more emphasis on alchemy to almost entirely Esper invested with just smoke bombs for start of fight utility, but while the game incentivizes focusing on a tree, I think Alchemy is probably the objectively worst to focus on early game, as it has pretty much no damage per turn in comparison to the other two branches outside of AOE in large groups, but even then, at least at the stage I'm at (Working through the city core), most fights either are solo, have at least one big enemy that's beefier than the others so it's effectively a solo with extra low health mobs, or don't have enough enemies to where AOE would be better than multi-attack, since even in group fights, it's better to just take enemies out as fast as possible by focusing them down so you don't take as much damage each turn, than it is to tank hits from all enemies multiple turns just to kill them simultaneously.
All this isn't to say that alchemy is bad mind you or that any of it needs tweaking, but Alchemy definitely feels like it fits better as a supplement to whatever your main playstyle is, rather than focusing a build on it.
Smoke bomb is great for example, and it does add a great secondary defense while still dealing damage at the same time, but when I was more heavily geared towards alchemy early game, I was either losing or barely scraping by in most fights-
Now that could also be because I focused on upgrading the cauldron as fast as possible early game, and maybe just wasn't investing as much in alchemy, but with a lot of encounters being mainly "boss" focused rather than "mob" focused unless you're farming cleared areas for some reason, 30%-60% DOTs and AOEs aren't exactly gonna be the most effective thing against the single tanky target with typically a couple hundred HP, in comparison to phys builds which have 80%-100% power attacks at base, and Esper builds that have multi-hit ability which makes them viable against both groups AND single targets, possibly even stronger than a pure might build in raw damage output, since 40% hitting a single target 3 times is really just 120% damage delivered differently and with extra scaling potential based on lust conditions-
But yeah, I don't think any of this is really a complaint, just kind of a side effect to each leaning into different niches.
I do see a potential "fully optimized" build though that would basically just be Esper, with dips into alchemy and might for extra passive skills and maybe utility.
That being said, with the game allowing you to pretty much change your playstyle at just about any time, it wouldn't really hurt if the game implemented more fights tailored to highlight the strengths of each style, just with with a bit of warning to the player to prepare for challenge encounters, and they may be better as side things.
(Also I'm still relatively early in the game and haven't even gotten Tempest to 100 affection yet, so...could be possible all this is already factored into the game in later fights, but I'm a simple man, and I like to rant about the game I'm enjoying so much, even if I am optimizing the hell out of it.)