But do you really want to just fight a generic Mob with extra abilities or fight a completely different thing in general.
Not sure how possible this stuff is. but possible future quest boss
There is definitely some good possibilities for custom mobs depending on how creative you are. Unfortunately you can't use any models that aren't available in Vanilla Minecraft. So one possibility would be like a possessed spirit sword. Basically an invisible mob holding a sword (cheesy but you get the idea, haha). Particles can also be used to help make custom mobs but until 1.9 they have to be used sparingly.
In general though big quest bosses or dungeons with custom mobs would be very cool. You could even imagine special items being available as loot at the end of a dungeon or quest.
I did some work with custom mob spawners. Just edit the NBT tags and out pops mobs covered in whatever you want them to be. One of my favorites were the frozen miners which were zombies is blue leather armor with a pickaxe and block of ice on their head.
I tend to not count command block creatures as a real option due to the fact they can seriously impact a server's performance. Command blocks themselves are incredibly inefficient form a performance viewpoint so limiting their use is important.