The userbase of the 3DS is a nice thing for Nintendo to have, but I don't think it has much to do with the discussion at hand. By it's very nature, the 3DS version would never have been able to have all of the features the Wii U version has. So install base doesn't really matter. Nintendo made the best games they could with the consoles they have on the market.
I think the staggered release was appropriate. I think Nintendo probably wanted the 3DS version to come out even earlier in the year, like July or August, in order to give the game some additional breathing room. It really only has six or seven weeks before it's superior counterpart is on the market. But, it is what it is.
I think ultimately the Wii U version will sell as well, if not better than the 3DS version, because of the quality of the title, and also because Smash Bros is very much a "play with everyone on the TV in the living room" game. You can kind of already see that in the sales of the 3DS version. A lot of people are clearly holding off and waiting for the console version. I didn't think there would be a lot of double dipping and I don't think there will be come November/ December either. Amiibo being Wii U-only at the moment also cements that.
Smash Bros 3DS has sold through to... roughly 6% of the 3DS base at this time? That's really good, but I think the percentage of Wii U owners and new buyers of the Wii U getting Smash Bros will be significantly greater than that. I think it will sell more consoles and be owned by more Wii U owners than Mario Kart 8.