Honestly, I don't think we ever see enough of either force to make a fair judgment.

The SOLDIERS you meet in game are tough but are still beatable by normal human standards. I mean even badass, "in a smurfing league of his own" Sephiroth was beaten by Cloud who is anything but a proper SOLDIER. So I don't believe SOLDIER is nearly as good as VII fans would lead you to believe. Hell, the Turks can hold their own against 1st class SOLDIER types (Cloud, Kadaj, and Zack) and they have no serious modifications whatsoever.

SeeD soldiers have more training and many are child soldiers (meaning their lives revolve around being soldiers rather than civilians with military training). Their services are sent in to deal with losing battles so they have a better reputation than SOLDIER. We never get an in-game assessment of what the GF's do for them so you can't honestly debate how powerful they are unless you use in-game mechanics at which point SeeD is obviously stronger. Even then, its still debatable...

Overall, we don't have enough info to pick a clear winner so it comes down to personal taste at which point I am voting for Magitech Soldiers would kick both their sorry asses!