I'm glad to see people looking at booking elsewhere, some discussion on the
Rewards discussion thread about Quidco cashback which may help you to decide.
The only time it's worth booking on the VTEC website is for their own advance fares. Even so as the online discount seems to be 2% everytime I've compared it's not in my mind worth bothering with.
It's worth booking everything else elsewhere because the only chance we have of reinstating the rewards scheme is if they see their commission dropping.
If you want Nectar book with a FirstGroup website. They give points for everything (quite rightly because they earn commission on the sale). If you don't care about Nectar or Quidco then book on a site you're happy with that doesn't charge fees.
The FirstGroup, Govia and Chiltern websites use WebTIS so have the same UI as East Coast. Others are based on thetrainline, but unlike thetrainline itself don't usually have fees.
personally, I've stuck with EC, I'm used to their layout, I like booking specific seats and I like the nectar scheme as well.
Of course, I keep forgetting about seat selection. That's one good advantage of booking VTEC tickets through their own site, but you should still book other rail journeys eleswhere particularly if you like Nectar? (not sure how anyone can like it though, better than nothing is about the best I've heard it described)