Sorry for delay.
# of masteries and # of skill slots in mastery is different things for sure. So, at this moment is already 10/11 masteries. I agreed, what there is limit, but there is not the end of the world. Since game intended to combine them - you already get more than enough combos which single person can personally try in reasonable time. If there is not enought - there is possible to make few versions of mod which allow different choices.
Skill manager / # of skills in mastery - there is limiting factor. In my taste - it should not be locked to around 30 (?) slots. Not for filling grid, but for implementing hidden bonuses, which might come from items. Similar concept already used in current mods, but number of hidden skills are limited, and them usually becomes generic by this reason. Monster slots also need care. Adding traits to monsters requires (rarely) redesign global passives to fit in limit. As for monster attack pattern it is even more important, as it allow i practice interesting chains, but there is not impossible do anything sensibly / not too repetitive so hard.
DoT stacking is also issue. Basically, instant damage is always win for player, but DoT can help with scaling (so you brand new AoE yet another flash freeze will not disintegrate mobs, and instead, say, let them live few another seconds which is big difference). DoTs in TQ are not used (mostly), and has so hard rules for stacking what no one exactly know and if we speak simply - it stacks only for weapon attacks and passive attack modifiers and procs except truly weapon based skill(s) (in sense where skill uses weapon damage + own bonus: throwing knife and ternion?).
Any way, this simply blocks to use, say frostburn instead of cold for true spells or you should trade, what your frostburn weapon attacks will not stacks. This on one side might add additional layer of challenge, but on another - this makes what you should choose one or another, but not both (exceptionally if possible damage are equally splitted). And this mechanically just unclear to utilize in practice except cases when player can write formulas about game mechanics just from heads, but this kind players is smaller part of mod audiency (and game is not self-explain cases enough).
This ruins possibilities. Imagine if your skills will do only 10% instant damage, and 90% as DoT over 5 seconds. Believe me - game significantly be harder. But this not implementable in a good way in TQ. But there is good scaling knob, but is not available in normal sense, as explained above.
There is exist also issues in how game spawn "proxies". Really, it is random stupid mechanism. The issue, what proxy limited what it can spawn, and if we want to provide better monster levels - there is not possible to limit choice based on PC level. There is exist few knobs, but they might work only in a way of puzzle art. {Also anyone seen what everything is heavily underleveled without PC do any farming, just at warcamp and till to end of act 2, except few creatures}. Is just broken PC progression, but this is also limited spawns issue (not flexible enough). Both can be fixed without engine modification - but titanic work needs here. Help from engine will make this things much easier.
Well. I'm bit going too deep. For me for years main thing what i'm prefer play in melee, but there is absolutely unknown why archers ignore OA/DA mechanics. I mean, as long as you kiting with backup bow, nor your OA nor your DA matters at all, as well as enemy stats. But if you melee - you are must have both to hit things. Ugh. Again, as long as you doesnt focus on phys/pierce damage - you can ignore OA, and keep it at reasonable minimum, because other damage types can't crit. So, best thing which some mod might implement (easy to do) h in favor make more choices equally well - is disable OA/DA mechanics for everyone.
And this might work. And even be way more hardcore than it now (with fixed crit simulation).
But this kind of balance even in own free to anything mod, this things overally makes me feel creepy. Anyway, I'm feel lot of limits, but never in number of masteries.
PS: All of you has good reasons / samples, I'm just attempt to add few alternation.