These are two tower defense games, although they are very different. Both are pretty good, but this is about the mistakes in the game.
Rogue Tower is a very classic tower defense game. You start with a fortress that must be protected and you build defenses or towers around it to defend it. Each round the map is extended, which gives you more room to build towers, can open new avenues for enemies to attack and can open up new opportunities for different kinds of support buildings.
After each round (or wave of enemies) you get to upgrade your towers, open up new towers or building, or other abilities. Each game gives you XP, which can be used to change what upgrades are available to you. The problem with this is that you only get a certain number of random options from which to choose the upgrades in-game, so when you use XP to open up new upgrades, you are less likely to get the one you want when you are actually playing the game. You can’t remove these options either without completely resetting your advancement, including losing all your accumulated XP.
Orcs Must Die! is a very different take on the genre, because where in Rogue Tower you look passively as your towers do their work during each round, in Orcs Must Die! you can (and should) take part in the defense actively. It is also 3D and has some pretty fun worldbuilding. (I personally like the way the characters approach a very serious threat by having fun with the situation and enjoying themselves.) Instead of towers, you buy traps and use them to either control the flow of enemies or to kill them.
In Orcs Must Die! you gain skulls from each game depending on how well you do. You can use these skulls to buy access to new traps or upgrade the existing ones. This is very flexible in the sense that you can reset all upgrades or even single traps (or weapons) to regain the skulls. The problem with this is that after you have a certain amount of skulls, there is no actual need to get more. You can always just restructure everything, but it takes time. You can’t do it within the game, so what you often end up doing is going into the game, exploring the map and then quitting the game to upgrade the traps you need for this specific case. It just leaves a weird taste in your mouth when you have to do this extra legwork to go back and move things around.
On the other hand, if this wasn’t the case, that would be a problem too. You would either save up the skulls, because you are not sure where you should use them, or you would use your skulls and regret it, when you use them on a trap you end up not using much or you are using, because you upgraded it, even if it is not optional. So, their implementation of the system is better now then not letting people tinker with their choices, but at the same time it doesn’t really feel good either, because of the clumsiness of the system.
I do have another problem with the skull system as well. Each map gives you up to four skulls based on performance (how well you defended your rift), one extra for being fast enough, one extra if you achieved a new personal high score for the map, one extra if you gain the biggest personal combo kill for the map and one extra if you get the best personal kill streak for the map. This is fine in some ways, but it also encourages some weird behavior. If you want to farm skulls, you should take the first map and be shitty with it, so that you can get the peronal high score as many times as possible. At the same time, if you don’t come up with this idea immediately, you can easily miss this farm by being too good. (Not that you need it, although I have gone back to the first map just to get enough kills with various traps to open up special upgrades for them and sometimes to test trap setups.)
Do I have solutions to these problems? No. I guess you could fix Rogue Tower quite easily by just giving the opportunity to shut down certain options for the particular run, which is something that does happen in some games (I just can’t remember which). Orcs Must Die! is a much more complicated case, but I do tend to play those games so much that it doesn’t matter as I have already upgraded everything I’m ever going to use, but it is pretty bad until you get to that point. You might even feel cheated if you didn’t realize this option is available to you.