I thought stat changes were intentional, which is nice. As you said, many Tower Defense games with combining gimmicks often are just so you have to spend more time playing the game (Padding) , with usually spending money to make it faster. But with the stats changing depending on the combination, it really allows a whole new level of strategy. It reminds me of the PvZ2 mod, Eclise. (Instead of leveling up plants, you can select tiers with different strengths and weaknesses.)
There's a different kind of challenge with this game, and it's the ability to control where the towers fire, without the need for the enemies to get within range. I agree that the some of the joy of a good Tower Defense is laying the groundwork, but most of it should be from the success of a great strategy. Mid-level should keep the player on their toes, but also allow them to prepare for the end wave. (Which, understandably isn't coming, so I suppose this argument doesn't work here...)
I like what you did to stop the AFK grind, which was the enemy that went straight for the towers themselves, and not only stopping the one hit, but blocking all shot behind it. It makes the player stop what they're doing to deal with it. I believe a way to challenge here, it to add special units the player must focus on. This is entirely okay, because the player has full control over where they shoot, but makes them unable to just leave it running for as long as they want. But then again, I'm no game theorist, so take that with a grain of salt.
For the mouse lock and lasers I have a few words. The mouse lock, in my eyes, is just there so the player can grab some towers without sacrificing DPS. But now that I think about it, having that struggle to let off the heat to get more towers, or risk getting overrun without those towers seems pretty fitting for what you have here. The lasers are pretty fun (and funny to be honest) and I believe you can keep it to one unit. If you set a limit to how many Fire Ups the towers get, it'll stop the lasers completely. But here's the kicker, don't add the limit for the Scout. Seeing as they already have a high fire rate, they're the first to become lasers anyways. You get to keep a laser, but the players also can't make everything lasers, win-win!
To end this off, I have to say that it's nice to see an attempt to branch out, not many are too fond of changing to a different engine once they've been working with one for so long (myself included.) Unity's pretty good, not be the best one out there, but it's up there!
P.S. - I really didn't do anything, this one's all yours. Your concept, your ideas, your game. All I did was saying what I thought out-loud (or in this case, typing.) Anywho, keep up the good work!