Same situation with starcraft here, but wouldnt say I dont like it, but I prefer the C&C series.
I think it all depends upon when you came to the series'. Personally I only came to Starcraft recently (last year or so) and I don't much like it. The definitive RTS for me remains C&C the original which, on an 8 player LAN connection (at school) rocked despite the tendency to experiment with cheap tactics (chinook with commando anyone?)
Similarly I regard Fallout 1 as being far superior to the sequel for storyline, novelty and gameplay. Fallout 2 is just more of the same without the novelty or cutting edge! If you came upon them both at the time of their initial releases I reckon Fallout1 and BG1 wiped the floor with all comers including their sequels!
I'm also with you in terms of Fallout, but I missed the better NPC handling from Fallout 2. I wish Troika could redo (not completely remake) and polish Fallout 1+2 a little (fix broken quests, adding new stuff etc.).