My "My Collection" is now full of "almost duplicated waypoints" (same name followed by a number), waypoints that may be unused, etc. Additionally, when I go to draw a new route, I have no idea what waypoints exist and where to find them. In short, the waypoint database needs serious housecleaning. This applies, to a lesser degree, to routes, too. According to Garmin, there is no database editor or even listable directory, showing what waypoints are where. Does this tool exist as a third party tool?
USCG has very definite rules about what goes where, even which AtoN's (USCG-speak for buoys, day boards,range marks, etc., etc.) are lit, which aren't, light characteristics (how often what blinks, how long its on, etc., etc.). Even so, things just don't quite come out as we end users would like. BTW, it's not uncommon to see a run of AtoN numbers get into triple digits. The southern stretch of the Intracoastal Waterway (ICW) has a few of them, for example. It's all great fun. Um-hm, yep, it is. [/<sarcasm]
(This going to get messy, even multi-quoting doesn't help out here)
Garmin's documentation, in general, is lacking. Some of the manuals just about list options and let the user guess what to do with them. BC is the worst of the lot. For a major tool, that should be a selling point, they could do much better.
The original clutter definitely came from thinking there was no hope for multiple collections. Armed with knowing multiple collections are possible, a lot of projects will gradually drift into focus as they're ported into their own collection. Or they'll remain in the Collection from Hell, which is unlikely to be used, save for looking at some old tracks. Uploading multiple collections into a GPS is its own "reward". As you say, doing so poses problems. OTOH, I suppose mixing travel in one area (SE PA) and another (New England) isn't likely to create many waypoint collisions. Given the limits on storage, there's incentive to not be a data pack rat.
I'm still tinkering with the "master list" concept. In a sense, though, I have that in list "everything". What it didn't have is the stuff from "ACT 1603" (previous trip). It does now. What's interesting is what happens when a route "test" is drawn in "everything" and it's copied to a new list "trial", "test" brings along a listing of all the waypoints in "test". All of this makes the drawing process easier.
All of this comes back to a lack of written support (documentation including examples). It makes for a steep learning curve. :)