It seems like there is no easy way to get that Peach-flavored cake you wanted...
You will enter a rectangle room. The room is split into two parts by a horizontal lighting-bridge.
Everything is portalable except for the sides of the top half. Bowser will basically be his own self; he spits fireballs at you and throws hammers (just less frequent). He stands on the bottom half of the map. GlaDos will be fixed to the sides of your screen, moving up and down along them (she switches sides by going off-screen). Her attack (in this round) is a horizontal laser that she uses from the top of the room to the bottom.
Your goal is to hit Bowser on the head, from above.
So you need to shoot a portal at the ceiling and underneath yourself to avoid the laser, then be quick enough to hit Bowser with GlaDos' laser by shooting a portal on one of the sides of the bottom half of the room. So basically you redirect GlaDos' laser by using portals to both avoid the laser and hit bowser. The top portal needs to be right above Bowser while the laser passes over the portals though.
If you either hit or miss after GlaDos' laser passed by and Mario is stuck on the top half, she will go off screen after a short cycle of Bowser trying to hit you with hammers from below. When GlaDos goes off-screen while you are on the top half, she will turn off the light-bridge for a few seconds, so you can repeat the cycle once more (up to three times would be the 'Shigeru Miyamoto standard').
Some notes on the first part: Bowser won't 'spam' his hammers as much. GlaDos sometimes switches sides after going off-screen. An optional thing could be that Bowsers shell will block GlaDos' laser, so you can be safe if you aren't ready to portal away from the laser. You will easily be able to see the laser coming, it's not too fast and it goes from top to bottom (maybe going fast and slowing down as it comes closer to the ground to give you more time to set the portal to hit Bowser).
So once Bowser received some hits he will 'die' and his remaining shell will spin on the bottom half (preferably a bit slower then regular shells, but bigger and with spikes ofcourse), allowing you to use it as a projectile to hit GlaDos, by using portals.
As soon as Bowser is dead, the room will change, turning all blocks to portable blocks, the bridge will still be there. GlaDos will still fire her laser from top to bottom just like before, but there is not Bowser to hide behind, so you need to avoid the laser completely. She will now fire fireballs at you as well, bigger versions of Mario's (heck, maybe even a companion cube on fire, goomba's, anything to avoid really). The same laser will now bug you vertically as well, forcing you to portal quickly.
The strategy to this is you put a portal on the top left or top right of the room (there where the blocks turned into portalable blocks) at the moment the bridge is gone and GlaDos is at the bottom (GlaDos will turn of the bridge for longer during this part of the battle and she is usually low enough when she starts firing fireballs or whatever).
It's a pretty basic idea, but simple and fitting the style/scenario.