I've come to believe that this is mostly dependent on just how you plan to play and how much time you want to put into it. Yes, physical skills are much more easily trainable and it's generally better to concentrate on certain others, notably Intelligence, if you want a better more rounded character in the long run...but also remember, 'in the long run everyone's dead.'
Intelligence will determine just how many points you will get from classes and reading books, therefore it's important to get that stat up to about 60-65 before you start your classes and books. There's a point, I forget just exactly what it is, where you max gains from intelligence so it's not helping you much anymore, if at all.
Charm can be gained up until 70 by Caressing during seduction and up to 85 through plastic surgery at the Doctor's office in Crystal Heights. Thus one might be tempted to forgo Charm in character creation as it can be trained up or bought later, but consider also the opportunity cost in that. Early charm makes the whole game much easier in the beginning and opens up doors much sooner affecting all facets of the game. Being able to charm Rebecca in the beginning to access the Space Marine soonest allows you to take out the highest level targets much quicker and easier.
Manipulation is not nearly as easy or sure to train as Charm, but you can get oodles and scads of Manipulation from books and there's diminishing returns on anything much over 100.
I find melee combat to be quite useful, my current Rise from the Ashes character seldom fires a gun anymore and I've critted myself up to a Melee Combat skill of 276, but also still fires a plasma gun on occasion if the target warrants it. The leader of the Highwaymen of Darkmere always tastes plasma as does the King of the Ceilor Forest Raiders as why would I want to take a chance on them firing that coilgun at me and my team? Top level bounties get similar treatment, but mostly my character uses his powered katana as I don't want to pay for the ammo and I don't need to use a gun except on top level targets like the above.