I suppose it just depends on one's perspective. For instance Fedor took on Henderson to ensure a win and keep his record good. Big mistake. He gained nothing from a victory over Henderson a natural middleweight. And he lost everything. GSP is a much smaller guy, and everyone expects Anderson to run through him. Problem is, GSP is better than anyone at middleweight he's faced in the aspect of the game were Anderson is weakest. GSP doesn't get submitted. He has the best TD in MMA. The best guard pass in mma. He's got very good standup defense. He's incredibly strong, perhaps the strongest WW in mma. On top of this, Fedor did not have to cut weight. Anderson will have to, and has not performed well and lighter weights (at least not as well as he has at MW).
It's not a good career move. I think he's likely to lose this one, and possibly lose it badly. If GSP can take him down, it's going to be a long embarrassing night for Anderson. If GSP can trade with him and avoid serious damage like Sonnen, ditto.
OTOH, Anderson would have much more success at LHW. He'll have his speed advantage, he'll have his energy. Now Jones is also a terrible matchup for him, but he will have his speed advantage, to be sure, and Jones doesn't have the same explosive GSP takedown. Personally I think he has a better chance against Jones. Wow, that even seems crazy to me and I just wrote it, but that's how I see it if I'm honest with myself. I think the dude will regret this decision, if GSP shakes his hand.
Okay, say everything goes as such and Anderson loses. Why was it bad for him? Anderson will no longer have the "but what about GSP" thing following him around. As I said, for someone so legacy driven, Silva would prefer to be the 2nd greatest of all time rather than the joint first (if it was a fight that could have been made). I think win or lose this is an amazing oppertunity for these guys. A once in a lifetime fight that can't be passed up. Do you think George Forman regrets fighting Ali?
I can't get my head around your scenario though. "Anderson Silva has a better chance against Jones than GSP". I can't understand that in any aspect.
Vs GSP, I think it will be easy for GSP to get a takedown at some point. He's not like Chael Sonnen however. Chael rushes you, puts you off and gets you down (if you have Silva's questionable TDD). GSP likes to work his way in. His takedowns are planned out and not rushed. All the while, he's standing up with by a mile the best stand up fighter to have ever walked on the planet (Bruce who?). It's the distance which I see is the key factor here. How does GSP get in without being touched? He will be left on the outside for a while, and as Vitor Belfort will tell you it's very easy for you to nudge yourself into range. GSP doesn't have the Dan Henderson style of getting in close and threatening with the H-Bomb. AS will give zero respect to GSP's striking, so I don't think he will even get near AS after a while, and it eventually ends with a great knockout.
Vs Jones, I see things going very different. As much as it kills me, I have Jones winning. Anderson gives away a lot as Jones is basically suited for HW. I think Jones keeps his jab out, lands some shots, and if it gets closer, he catches Anderson off guard by switching to a grappling/wrestling style. Although, it's still a stand up fight and it's still Anderson Silva. It's very easy to see AS coming up with something, getting his range right etc. He might be able to do a super version of Machida's strategy. He could stay on the outside and bring Jones in. If he lands leg kicks and beats jim to the punch or whatever, it might annoy Jones and make him come in more aggressive, where we see a Griffin x2 knockout for Silva.