I like both of them a lot! I think I like GemCraft better because of the strategy. However, I really like Bloons TD 2 as well because I like Bloons and it is another great step for ninjakiwi. They both bring something different to the table and it seems to be a matter of what you are looking for in a TD game.
Bloon's #2 is too easy. All you really do is place some dart towers, a cannon or two, and put road spikes back beyond their firing range.
Bloon's #1 has a similar problem. All you do is place a crapload of dart towers, and you automatically win.
However, both have a certain charm to them (IE, monkeys with darts, balloons, and bombs), and are very playable.
GemCraft is my personal preference, as it takes a bit of thought as to which grade of gem to place where (will the grade 4 be enough, or should I upgrade?), and the increasing cost of towers that makes placing towers on every open square impossible is a nice addition.