There are two different issues discussed here: the "thing" and the "action". I'll adress them separately.
The "thing". As has been pointed out, almost all sci-fi out there speaks of the limits to the amount of cybertech a body can have: Shadowrun and Cyberpunk are good examples of this. Of course, not all sci-fi does, Eclipse Phase has no limit, for example, and technologically-wise it would be closer to EVE.
So, let's imagine there is a limit of "slots" available. In such a scenario, then we would have pod-pilots using their head slots and spine slots on pod piloting implants (as has already been said), but they'd have their legs, torso, and arms free for implants there. If they installed combat mods there, then they would be above baseliners in ressources and everything, but below those that use all their slots for combat/stealth (for example, no cyber-reflexes as those would go in the brain or spine). They'd be good, but not impressive. Old-seph fell into this cathegory, he once lost a leg (I think he lost an arm too, I'm not too sure) and had it replaced with a cybernetic one, which he'd have in every clone, just to remind him the price to pay for what happened in the other side; then again, the leg wasn't rigged for combat (Seph was more a philosopher/spy than a warrior), but it could have been.
The other side of the coin is a universe where there are no limits to implants. On this side of the coin, nothing prevents an egger from getting cutting edge military hardware for everything he wants. Sure, damned expensive, but we all agree eggers are very-very-very rich, so it wouldn't be a problem for many of them. This would probably make them way above average, but still wouldn't make them optimal: a DUST soldier would still be inmortal in combat (which an egger isn't), have more experience, train more hours in physical things, will have fought in more scenarios, etc. But probably, below DUST or CyberKnight levels, pod pilots would be top notch (say, second league's best team!).
The "action". The key that arises most discussion here is how you use it. But actually you're all mostly agreeing: no godmodding, consensual RP. Which are the rules of good RP in every level (I can't go into a bar owned by another player and "buy it with my overwhelming wealth" even if we pod pilots are very rich!). So, as long as those rules are maintained, I see no problem with pod pilots being physical.
Of course, going down to land battles is probably pointless unless a real good reason can be given (knowledge of key codes or such they alone know and don't want to share, for example); it'd be useless because, as has been pointed out, it would be of very little use, compared to the help he can bring from orbit. I don't think soldiers would be happy to see him in the frontlines, like WW2 soldiers wouldn't expect Patton to be with them in front of a Panzer. That's what liuteneants and other low-ranking officers are for.
But that doesn't mean an egger can't be physical in other situations. I'm going to use a character I hate because it extensively god-moddes, but take Starbuck from Battlestar Galactica: she gets into brawls, sneaks around and assaults bars (in a horribly bad scene, btw!), etc. Not all eggers are cold psycopaths, not all are intelligent philosophers, or astute politicians. They all share one trait: not going into the wetgrave. That's it.
Catillah, for example, is a nice guy in his way, but he wouldn't have a problem in getting into a bar fight if he was caught in one. Wouldn't start one, though, but wouldn't stand idly and say "no punches please", but would pick up a stool and hit someone in the head with it. He's not physically improved by cyber or nano, but he is a soldier, and has some training in hand-to-hand combat and guns from his time in the Navy; doesn't use them much (in fact, he needs to ask his ship's computer where is his gun, as can be read in the "Who am I" story in the forums), but he does know how to.
Is that wrong? I don't think so. As long as I say "I get up from behind the bench and start shooting against Bla Pilot" and he gets to do what he likes on his end, we both agree to consensually, don't god-mod, and, in general, have fun while doing it. And, of course, accept the consequences. Catillah was expelled from the Imperial Navy without honors, and this was one of the reasons (the least important one, though).