Good moral usually has all the perks.
NCR, Brotherhood (Untie the two), The Followers (Untite them with the NCR too), and all the other good factions.
To be frank I would go with speech, med and guns, but dont worry if you get all DLC you will have alot of time to upgrade...alot to the max, my guy is invinsible, BWHAHA.
But ill list the best ones.
Speech - Can convince people for you advantage (Get 100 and you can do anything with your mouth)
Meds - Some of the best quests have you healing people, so its a good one to get for yourself and quests.
Guns - Obivously you would need this to kill everyone, guns are the most common thing you find out there (Exept for malee, but against a deathclaw, your screwed!)
Also spend time to upgrade, repair,
Others:
Barter - (Reduce prices)
Explosives - (More damage to the g-nades and all, also a few quests can be solved with this)
Repair - Repair weps, armour and also for quests.
Unarmed - Awesome punching without repairs or ammo
Also make sure its suited to your playstyle, thats works out the best, I play as a member that can talk, barter, shoot, heal, punch my way out of anything.