Specializing in Magic Theory is fun, if you want to go for the Magic Theory Integration plot thread (ie, optimize on making a successful Magic Theory Integration roll vs. an 18). At which point you probably NEED to have generalist arts, as the Insights you develop can potentially be all over the map. Or at least, a really good general Lab score: high quality equipment, optimized on spell creation, with a lab assistant or two and a familiar.
You forgot a tricked out lab.
Well, if you routinely need to Penetrate to use your magic, you either have a specialization in the penetrating magic, the magic is easy-penetration (summoning with True Names) or you're doing something wrong. And every magus should definitely develop a niche in their covenant that they do better than anyone else.
That said, one of the more effective ways to be a magical combatant is to not use magic in battle, as has been pointed out both upthread and in HoH:S; specialize in Parma Magica and combat skills and you can be a quite lethal mage-killer, and while there's likely to be a strong Muto component to this, it doesn't need to be especially high for most of what you're doing and you certainly don't need a magical focus for it. Use the rest of your XP and study time on whatever you want.
Also, a Magic Theory+Int+Apprentice+Lab is the specialization of the generalist. Being able to make small-to-medium spells of any T+F is not an ability to discount...again, Penetration is only relevant to spells that have to penetrate.
Heh - well, technically I forgot to put the word "lab" in there, (right before "optimized on spell creation"), so...yes. I did. 
There are also certain magical specialties that take a while to germinate. It could be a focus that doesn't align with a lot of canon spells and requires inventing all one's spells. The pacing of the saga is also going to have a great determinant as to whether these specialties that require time will come to any sort of fruition.