We went to Thailand last September for our homeymoon, had three days in Bangkok and a week on Koh Samui.
I wasn’t too fussed about going to Bangkok, I don’t really like city breaks, prefer tranquility etc, and when we first arrived (jetlagged and tired) I hated it. Noisy, smelly, so busy. It really grew on me though, and in retrospect I think I prefered Bangkok to Koh Samui. It’s hard to explain why, but I have friends that have had a very similar experience.
I would strongly recommend “cooking with poo” (google it) as something to do whilst in Bangkok. She’s amazing, and you get a glimpse of the real world that you so rarely get on holidays.
As for the rainy season thing, we had a bit of rain in Bangkok, but very little in Koh Samui, apparently it’s not so rainy there in September (more so in Phuket though.)
We found Koh Samui to be fairly touristy and a bit grubby, not quite the tropical island that we (naively) expected. It was still a great holiday though.
HTH.