Grappling with this one myself and interested to hear opinions.
Just looking at the fronts, brand new 2.5's from Rockauto are $676, add $84 for hats, $475 for Giesers and I'm at $1235. New Gen2 fronts with Mikra bodies is about $1800, add Giesers and it's $2275. A new pair of Fox 3.0's with DSC is about $3k which of course include springs (albeit maybe not progressive so Eibachs on the other two may be a more accurate comparison, about $175 less). Or there's whole hog mid travel with bypasses, but jeez at $15k that's spendy.
Supposedly the Gen2 shocks will have a longer useful life before needing a rebuild, makes sense to me as the tech is newer, the larger diameter should translate into less stress on components, but ultimately everyone's mileage will vary there. Plus you're starting with brand new shafts, bodies, etc. By the same token, new 3.0's should also last better than stock 2.5's, especially with the addition of the remote reservoirs, I would think under the same use they would last even better (which along with adjustability is the main justification for the expense). Then there's the question of Live Valves and the Eclik system, which appears doable on a Gen1 but you're pretty much in 3.0 price range and not sure if you're better off.
I'm thinking I'll try going with new 2.5's and Giesers, so I'd have a spare set to rebuild, and skip the Gen2's in favor of 3.0's in another year. But still on the fence...