Fernando,
If you search through the forums for old discussions about cooling issues, you'll find various opinions. The general consensus is that when the cars have been maintained well and all cooling passages are unblocked, all the models should fare reasonably well under stop-and-go conditions. However, all models start getting warmer the longer the car is kept standing.
Every model is slightly different:
230SL -- closest to original engine design of the 220, no oil/water heat exchanger or oil air-cooler (although exchanger was available as an option-- for hotter climates)
250SL -- oil/water heat exchanger added as standard issue
280SL -- higher power, fewer water passages (to allow bore increase), but added oil air-cooler next to radiator
Maintenance is a bit more involved with an automatic, but appears straightforward from what I have read in these forums. A manual transmission has no oil filter to replace, and no connection with the throttle, no kick-down, etc, etc.
Both my 230sl's as well as my 250se/c have manual transmissions, but that's my preference. I feel a bit less in control when driving an automatic. I think you should go with what makes you most comfortable driving.
As far as A/C is concerned, neither of my pagoda's has that engine-bay disaster. I'm currently in the process of converting my 250se/coupe from the U-boat era York compressor to a Sanden rotary unit (the York had sprung a leak).
From what I remember, my experience with the A/C in my coupe was similar to CarlG's with respect to stop-and-go traffic. While cruising, the temp needle has always behaved.