Some friendly suggestions?

So I've been working on my game (though not as much as I wish I would) and I had a couple things I was hoping to get suggestions on!

-My first boss battle with multiple people seems balanced to me, but when you get to the point where there are TWO (or more) BOSSES rather than a boss and minions it gets tricky. I don't want the player to kill one of them and then feel like the rest is a cakewalk, so I made it so that whoever is left gets some upgrade and an invisible NPC to add attacks. However, I feel that if I use this in the future, it would become overdone and almost feel like I'm just cheating to give the player a hard time. Any suggestions?

-This is something that I was tempted to put as my bug-fix, but perhaps there is a way around it because I could see it being annoying in a lot of people's games- the buffing/de-buffing system. Is there any way to plotscript or something to get around the overwriting thing? It makes buffs feel so useless when you pump up your defenses, then you see a debuff which not only lowers it, but sets it to ZERO first. This also lowers the coolness of a typical dragon warrior last boss move, the one that eliminates all status effects. Any way around this that anyone knows of?

If I think of anything else I'll edit my post to say such things, but it'd be much much appreciated if anyone could help out! Thanks in advance!

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You can't fix stupidity.

For your first problem, you can also increase a boss's difficulty by giving it powerful Alone attacks. This also works with regular battles and is a good way to make them a little more interesting.

Another approach is simply to end the battle when one boss or the other dies. I can think of a few examples where this is used well (Masa/Mune in CT, Rooftop of Riovanes in FFT).

Yet another approach is to present the enemies serially instead of all at once -- think of the Four Fiends battle in FF4. This may be tricky to fit in with your plot, but it's worth considering.

Finally, you can balance it so that the battle isn't a cakewalk when you've eliminated a boss. There are several ways of doing this, too, but the two most obvious methods are:
- regenerate the missing pieces (Guardian/Giga Gaia in CT, etc.)
- make the enemy you want to get rid of hard to kill. For example, if you have an attacker and a healer, you'll want to kill off the attacker to prevent his attacks, but he's hard to kill as long as the healer is there. (You'd want to give the healer Alone attacks so he's not completely useless when alone.)

^-- I might think too much about this stuff

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Mega Tact v1.1
Super Penguin Chef
Wizard Blocks

Mogri's suggestions are about as good as they get.

Mine are:

As an alone attack for either enemy, if they're not killed fast enough they revive the other. ( Similiar to the regen suggestion. )

Or have minions that are steadily spawned throughout. Even though it would still be easier after you killed the first enemy, the second one still shouldn't be too easy.