Continuing the discussion from Defender's Quest 2 - Weaselmancer and cast preview:
Took me a moment to find this fabled feature of yours. ^^
My problem with the atomic A-or-B choices is that they don't often fix the underlying problem we were having with the old Skill Trees, that is, options weren't balanced. Even in Bastion, there was always one more correct choice for me, and often it boiled down to what I valued more, which often was what would make my experience with using the weapon better. Reload and ammo count upgrades were a major preference for the ranged weapons so that the reload cooldown would break my combat flow less. Removing bullet scatter was another one like that.
And this preference-based optimization never changed, so barring special achievement requirements, I never bothered with it ever again.
But this worked for Bastion because it was basically an effect of leveling up your weapon. You made it more powerful or you made it more like you wished it was, and level up done. If you regret the choice or something, you can go back and change that particular level, because it wasn't a talent tree so much as a build optimization. The builds being your two weapon choices and one skill choice.
The atomic skill tree in Wings of Liberty worked much the same way. It was catering your units to your play style. There was always one more correct choice based on power or play style preference, and once picked, you never wanted to go back unless you decided you screwed up or it wasn't what you wanted for some reason. And the three-way atomic skill tree in WoW bit me, because it was basically asking me to make a 'play style' vs 'most correct' vs 'least correct' choice. There was the talent choice I wanted to pick, the talent choice all the guides said I should pick, and then the choice nobody picked. This was more annoying in general, so I'm not entirely sure it was a gameplay improvement when I had to change my choices every boss fight or so to optimize my build against said boss. It became a situation of knowing what I needed to pick beforehand, and picking it whether I wanted to or not. That's not fun in the end. That's doing your homework, checking the appropriate boxes, and then either doing what you were going to do with the blue shield rather than the green shield or finding yourself with a character that's less fun to play as.
Which is to say that the basic atomic skill tree falls well short of what I think most people want/expect from a skill tree. Especially in a tower defense game, where it's integral to the feel of the tower becoming more powerful over time.
So coming from my Blizzard/Bastion/TD/etc experience, let me suggest something a bit different that somewhat incorporates the idea of choosing distinct tower upgrade paths. Plus some variations.
Everything costs 1 point to get, and I think an interesting idea that would make this work better is if each character got Skill points and then passive points. 3-4 Skill points total, so there would always be 1 or 2 skills a character didn't have, then a limited number of passive points to emphasize certain skills or abilities or synergies. Passives could be a mix between stat bonuses (Attack/Defense generics) or effect specific bonuses (Bleed power/HoT applied on Heal) or skill specific bonuses (Skills 1 and 2 gain increased armor penetration/Ice Skills get +1 range).
If you go for the atomic passive choices variant, you could probably do it like Bastion, where they have two or four or six ideas for the way a skill can develop, so the player can choose a mismash of these development paths they want at each tier.
I think this simplifies things down akin to what a simple atomic tree offers without completely sacrificing the diversity of interesting choices and possibilities that a more standard tree offers. A compromise between ease of balance and fewer, more potentially interesting choices on one hand and the desire for more diverse and tunable outcomes on the other.