The decision as to whether to make an ally an Extra or Wild Card depends on a number of factors.
The first and most straightforward consideration is how tough you want them to be. Making an ally a Wild Card significantly increases their capabilities, and you need to make sure they don't end up overshadowing PCs and stealing the spotlight.
Another question to ask yourself is how important the ally is to the plot. Typically, there should be far fewer Wild Cards encountered than Extras, whether they be allies or enemies. Don't forget that Wild Cards are special, and a cut above the rest. The more you introduce into the campaign, the less this will come across.
You mention Edges that give PCs Wild Card allies. This is a different issue to the NPCs that the group will generally meet as they are adventuring. Those allies gained by Edges are considered to be far more loyal and unquestioning in their relationship with the PC with the Edge, whilst general allies think and look after themselves far more.
The last consideration is combat. The more Wild Cards you have in combat the longer and more complicated it tends to be, as you have more to track and those involved take longer to put down. Also, the advice in the core rules is that allied Extras should be given to players to control, whilst Wild Cards are retained by the GM. This is a good general guideline, but I have found that there are circumstances where it doesn't hurt to give a Wild Card to a player as long as you can trust them to behave responsibility and given them actions in keeping with the NPC they are controlling.
When it comes down to it, different GMs use different ratios of Extras to Wild Cards depending on their personal preferences. There is plenty of wiggle room, and going a little too far one way or the other is not going to break the game completely. My advice would be to start cautiously, only introducing a few Wild Cards initially until you get a sense of what feels right for you.