Swift is at different level in all categories compared to Alto. I think you'll enjoy the ride of a 1200cc Swift very much compared to 660cc Alto (i have not experience both, but just comparing the facts they have on paper).
If you are okay with driving a manual after driving an AGS, i don't think it's a bad decision.
however, strictly from a resale point of view... Swift is not the best investment for resale. If only resale is your concern, go for Yaris or City manual