If a capital is the administrative hub of the country, it should have high "VP" value. If it's only a figurehead location, with the real administrative center elsewhere, it should have a lower VP value than the effective "capital". Just occupying the capital with a division of paratroopers should not automatically cause the country to capitulate; you should need to hold either a considerably majority of the VP locations, or have destroyed the vast majority of the army to get a full surrender.
Limited campaigns for limited goals, on the other hand, should NOT require occupying 75% or more of the country, merely that you have de facto control of the area in question and have defeated enough of the army to have a clear superiority. In a case like GER against DEN or BEL, a relatively minor battle should be sufficient to inflict enough losses to bring the smaller nation to the table for modest concessions, but their National Unity and their own national goals might limit what can be bargained without further fighting. Puppet, or ask for some resource concessions? Sure, simple Poker math: a loaded Mauser beats three of a kind. Annexation? Now it's not a game, and somebody's going to get hurt.
Granted, the final expansion of HOI3 had the same wargoal "system" as some other Paradox games, like the latest CK, but unfortunately HOI3 didn't have a complete set of wargoals available. Depending on what country you played, you might be able to ask for "region A", "region B", a puppet government, or complete annexation, but in other cases, the only options were to puppet or annex.
As an example: In HOI3, Hungary can demand the thin strip of its "cores" in CZE which were historically granted by 1st Vienna, or for all the German areas (all of CZE except Slovakia), but it can't ask for all of just Slovakia, or for its historical pre-Trianon Treaty borders (most of Slovakia). In essence, it can demand almost every combination EXCEPT what it actually claimed. It can puppet or annex Romania, but I don't believe it can even ask for its cores in ROM as a wargoal, and it has no way of asking for the rest of its pre-Trianon (and pre-WWI) regions within ROM back. The situation with Yugoslavia is no better, where you can't even ask for your cores, much less the previous borders. It's better for the majors, but still not great, since GER can't ask Poland for its pre-WWI borders, only for a paltry few "core" provinces provided around Danzig, or else they have to puppet/annex the whole country (they can get a few additional "cores" of limited value via the M-R Pact). The frequently disputed Alsace-Lorraine region is not included as a German core. On the other hand, Italy gets a ton of "cores" along the coast of YUG, merely because they wanted them.
Yes, HOI3 got a wargoals "system", but without most of the wargoals.