Well PF3 already has the option to prompt if wypts are too close. Which you can you turn on or off if you wish. In my fpl it isn't a "user mistake" and it works. Real flightplanning is very much a black art and one does not rely on software that "generates" a fpl. Many simmers are led to believe that becausethey have spent lots of money on a fpl programme that it must somehow be pukka. This is not the case at all. And it is a very steep learning curve to understand how it all works. Likewise ATC. The majority of simmers don't have an RT licence. It comes as a surprise to learn that in many European countries a pilot must pass the RT exam with 100%. Both the UK and Italian CAA's request a review if a pilot fails the RT exam to the point that the pilot training could be stopped by the authority.
What you describe is a "potential" mistake by the user. It really doesn't need PF3 to hold that user's hand. All the user needs to to do is adjust the fpl by adding a wypt or moving a wypt further away. Especially bearing in mind that the majority of fpls generated for sim use are wrong anyway!!
Waypoints too close as I understand in PF3 can have weird results. So, you should fix that. If I pilot and ATC can deal with close waypoints why your software can't?
Vectors to final: if my last waypoint is less than 20 miles I will have problems too. Well in real life is not like that. Wouldn't be better to have a few options in the connect window for choosing a)vectors to final and b) another choosing a percentage of occurrence and leave my original full flight plan. This way PF3 would internally remove the necessary waypoints if it chooses to vector me? If my waypoints are too close deal with it, maybe pf3 should internally check where is the aircraft in relation to these points and then determine which one are we flying to.
In real life we don't have to make 2 different flight plans, one for ATC and one for the MCDU as with PF3 (virtual ATC).
ATC humans are smart enough to deal with all that (close waypints, vectors to final before last waypoint, minimum vectoring altitudes, separations, ..). I think a software can be smart enough to do the same, and I think it will be a good goal for this program.
I like PF3, I just want to keep it improving hopefully in this direction.