Depends on what you're using it for. Early on, I like to sub WAR for the extra dmg, but later on, when I can't get a party because I'm a drg, I'm going to sub brd, not just because I love brd, but because every time I cast a song, the wyvern will heal me, and unlike any other magic, casting doesn't cost MP (or tools, in the case of ninjas)

You should take your own style of play into account. There are 3 different types of wyverns you can get, based on what subjob you choose.

Offensive Wyvern
Subjobs: WAR, MNK, BST, RNG, SAM, THF
These wyverns will attack using their breath weapon whenever you use a weapon skill, and have a good chance of discovering theh enemy's elemental weakness with their breath weapon. (i.e., against orcs, there's a good chance your bird will use water breath. This is more important in the dunes, when nobody has any lightning skills, and your bird can breathe lightning on snippers, which are weak only to ice and lightning)

Defensive Wyvern
Subjobs: WHM, BLM, RDM, SMN
These wyverns attack normally, but when you cast a spell, the wyvern will cast cure magic on the party and heal any status ailments that are present on you.

Balanced Wyvern
Subjobs: BRD, NIN, DRK, PLD
This is a cross between the two, and great for soloing. When you use a weapon skill, your wyvern will use its breath weapon, but has a significantly lower chance of discovering the enemy's elemental weakness. When you cast a spell (including bard song and ninjutsu), the wyvern will cure you (not the party, just you) and attempt to remove any status ailments