for instance: in maya I can build a character(model/rig/textures etc) and reference that file into a scene…but then later, replace the reference with an updated file or a totally different file…and provided I've been smart about naming things etc the new file will slide right in and use all the animation in the scene that was originally on the first referenced file.
If I build a character and export it as an OTL, then hand that character off to an animator, how would I get the kind of incremental control that I have with referenceing in maya.
You can do it the “maya” way, or with a less hands-on approach - whichever you choose. It's actually more flexible in Houdini. The maya way, as you mention, you attach a reference in a given animation file to a particular thing, an it scoops it up. Obviously, this requires some outside management to control what that file is - either a naming structure, or links, or whatever. You could do the same thing with OTLs if you choose - call a file foo_21.otl and reference that in your hip - and that will always load. Later on, you could change it to foo_23.otl, and that will load and maintain your animation. Alternatively, you could always reference foo_CURRENT.otl and that's a link always being updated tot he latest. This is the same as Maya.
OTLs also let you manage things other ways, too. For instance, you could always be loading “foo.otl” no matter what, and it may or may not be constantly updated, or a link pointing the the latest. If you're set to load the most recent based on datestamp, it will either use the last data saved in your hip, or the one on disk if it has changed - this could be automagic. No managing of file names and what points to what. On top of that, you have total control over the process - if the TD has screwed up and the changes they've made to the OTL breaks your hip(for example, renamed the channel names so your existing animation is broken), you can optionally stick with the one in your hip, on the fly, and keep working until the TD removes their foot from their mouth.

OTLs are really wonderful….
Cheers,
J.C.