The boss battle generator although cool is not without issues, it sometimes spawns bosses on entering (without any connection), and sometimes they can be either to punishing or just to easy. They also get stuck with terrain changes. Proper level design is necessary to have great battles (and punishing ones, as without checkpoints you basically have unlimited lives) I recommend spicing things spawning other enemies, or adding aditional conditions to the battle per se, like checkpoints, life counts, teleporting on defeat, and what not. Another thing is memory, make sure when you enter the boss battle that there aren't a lot of enemies left unchecked running around on the map, as they consume memory and may cause the game to run slow or just poor performance.
Hope this helps.