What software or planner are you using to construct your short Route? It rather sounds as though it's generating far too many points. And what map in the GPS? A Route of say 20km/12miles shouldn't require more than about 6 points, since you appear to be working in 'follow road' mode.
The main problem is ensuring the GPS in 'follow road' makes the choices you expect it to make, ie goes along the same roads that you planned. The simplest way to do this is to err on the 'more points' side, rather than 'fewer'. Unless, of course, you actually want your GPS to take you on a magical mystery tour.
In typical laney UK topography, it might be reasonable to aim for an average of say 1 Route point per 5km - so that the 50-point limit would allow you around 250km, or a very long day ride with a single Route. (Though with storage for 50 Routes there's nothing wrong with using 2 or 3 in a day.) But does 1 point per 5km really guarantee that you'll follow the planned itinerary? I'm not sure it does, in laney country. (It would in mid-Wales, or in most of France - but possibly not in Hampshire say.)
But certainly, I'd say, if you have points more frequently than say 1 per 3km on average, then there's something wrong - and that's when you get the 'nagging' effect on the GPS.
Others who use this mode more than I do (I prefer 'direct' mode), may be able to fine-tune these figures a bit.
You could approach it another way and assume that 1 follow road point should be able to replace 3 route instructions, ie 3 turns where you would need a point in 'direct' mode. I think that will give a similar frequency of 1 point per 3-5km, on UK lanes.
Another worthwhile tip for 'follow road' mode is to put your points on the roads you want to use, and not on the junctions. Leave all the decision places clear of clutter, so that the GPS can do its thing. Otherwise, the points you add will interfere with the instructions the GPS is trying to give. Try it both ways and you'll see what I mean.
This is the opposite of 'direct' mode where you would want to put your points on the junctions (or a bit before, or a bit after, depending on which of the three sects of the direct religion you belong to).
This is why, when planning a Route, it's best to have a clear plan of which mode you are going to use on the GPS.
There's no need to differentiate between User Waypoints and Route- (Via-) points, since your GPS can store 1000 User Waypoints which is loads - enough for 20 50-point Routes or about 5000km ...