Favorite bombs? They've never been my favorite item... far from it, actually. Some use them for combat I think, but me, I just use them for opening new areas.
But if I had to choose I'd pick the Remote Bombs from Minish Cap. Bomb Arrows are cool, and Bombchus/Bomblings (same basic thing) are great, but the Remote Bombs were the most practical for me. I liked how they served the same purpose but had great use in combat. I used them lots to fight tough enemies that were dangerous to approach, like Ball & Chain Troopers and Darknuts. I loved how you could use them while running, throw them, or use them like mines, and I loved how they let you control the situation much more than with normal bombs.
It seems in general bombs haven't gotten the overhaul like many other items have gotten, sorta. There still has been a variety, mainly in the last few games. The Arrows and Boomerang seem to be different in nearly ever Zelda game but not so much the bombs.
Yeah, you have a point. It's interesting. Bombs aren't something that can be changed too much though. Other items can be modified, but bombs kind of have to be bombs. Though as you said, in the last few games there are new kinds of bombs. I kind of like that, putting that spin on the bombs. I'd like to see new kinds in future games.