I think a Base class is appropriate if the mechanic is different. If something you can do by swapping out the class features of another class then the Archtype is warranted. Basically if you have to swap out all the class features it might as well be a Base Class.
I like alternate class features the best, since they're the most flexible.
Archetypes, base classes and prestige classes are all nice, but ideally they should follow a simple guideline: they should only be used to fill a missing mechanical niche, not as fluff-only changes or mere page filler. So if your new class is a fairly standard fighter/rogue/magic-user/cleric but from a different school/country/sect, for instance, that's a waste of space IMO. I could name a number of PFRPG archetypes, base classes and prestige classes that fail this test.
I want it all.
New base classes: If a concept fills a virgin mechanical niche such as scene editing, or time effects, swashbuckling via swift and immediate actions, or the like, their is no question that it should be a new class. I want to see new classes.
New architypes:
When a concept can be expand on the mechanics of a class that already exist, but is distinct and self contained, then sure.
Best for dealing with broad, non setting specific combat styles.
New alternate classes:
Like architype, but concept requires greatern changes to the base class. Also if said concept can support a range of architypes.
Prestige classes: As base class or alternate class, but with strong ties to a campaign setting and mechanics and background that make it in appropreate for starting characters. Example: bloatmage.
I'd like them all. the all do different jobs and all work best for certain jobs.
I like archetypes but I'm not feeling the full-class replacement things.