Pitiful, but at least it existed.
In terms of prominence - well, I take your point, but in 1589, there were 20-odd non-episcopal Dukes in France, and only two extant dukedoms were older than those held by Henri IV. Almost all of the others had been created in the last 50 years, and when all's said and done, the lands attached to the Dukedom of Bourbon - the last surviving major feudal territory - were pretty extensive.
@Matteo - well, the whole point of Henri converting to Catholicism was because the nobles and notables weren't sure that they wanted a Capetian on the throne. Hence the big war. A Capetian who was essentially a country squire, with none of the advantages which Henri IV had, would have even less support unless he was malleable enough to act as a puppet for one of the factions. As I say, there was some support for crowning Guise in the Catholic camp.
But a bastard is certainly a good alternative option, with the caveat that Joao of Aviz was a political genius, and even he had to fight a civil war against Castile and three other claimants before he could take the throne, and later on, the Prior of Crato had all the advantages you point out and the nobility of Portugal flocked to Felipe instead (at first).
So you make good points, but the truth is much less clear-cut than you present it as.