I think its going to vary on a game by game basis.
If you like adventures the CD32 versions of Simon the Sorceror and Beneath a Steel Sky make a lot of sense, no faffing about with multiple disks, and a cool talkie soundtrack. But Dark Seed is a disaster. The A500 version is in higher res, and supports the mouse which the CD32 version doesn't - criminal in a point and click adventure. Similarly the CD32 version of UFO: Enemy Unknown is inferior to the 1200 version. When you save it does not store all the information about your bases.
The CD32 version of Wing Commander is possibly as good an example as any of an improved production, it makes the AGA and ECS versions look horrible. CD32 Frontier is basically ECS but it is the latest version of the game ever written. The downside is that while it supports the mouse, occasionally clicking a mouse button in a base will cause your lasers to fire, upsetting the authorities and damaging your reputation.
In short, its a case by case thing.
