I haven't taken the RS tour so can't comment on that. When you said "Greek Isle tour" did you mean a cruise? I ask because you mention not enough time on islands during stops.
If you're thinking of the RS tour then you must have 2 weeks to travel so you could design your own island tour using ferries/flights to get from island to island and spend as many nights on each island as you wish. There are tour agents that can set this up for you. I've seen a couple of them mentioned (can't remember names) on this board so maybe you could ask for suggestions in a post on the Greek forum.
I went to Greece with a group on a customized tour and spent nights on 5 different islands plus Athens and a couple of other places on the mainland (Delphi, Nafplio). It was a wonderful experience. I was there in July, yes the mainland part was pretty hot but the islands weren't bad at all. I can't comment on travel there in Sept/Oct - that might be off-season there so may not be the best time.
There's nothing wrong with taking an escorted tour, I've done many of them, but you could do this yourselves also.
Happy planning and enjoy your trip to Greece.