I said all the games did it. The alliance has never had the most advanced technology in the universe, why would an alliance soldier have the best gear in the game anyway? Kassa fabrications make the best armor, they're not owned by the alliance.
Right, and all the games handled it badly.
Shepard isn't just some random soldier. Depending on the timeframe, he's either on the most advanced warship in the Alliance, a Spectre, leading a hugely important and expensive Cerberus mission, or leading the most important mission in the history of the Alliance.
Breaking it down:
1: Normandy doesn't even have the best Alliance gear. It's tolerable for a top-of-the-line Alliance ship to be worse than crap you can buy off-the-shelf, though it implies the Alliance is a very poorly-managed organization. 120 billion credits for the drive core, a few hundred for weapons and armor? Dopey, but tolerable. But Normandy doesn't even have the best stuff from the Alliance manufacturers.
2: Spectre. OK, this is just stupid lore. Self-financing agents who are above the law? I don't see how you could devise a more corrupt system.
3: Cerberus. So... TIM can't cough up a little more cash for the best stuff in the Citadel, Ilium, and Omega markets? I'll give Tuchanka a pass because, hey, who knew there was anything of worth there. Hell, Normandy doesn't even have the best Cerberus equipment; remember the upgrades from the Reaper IFF mission?
4: ME3: No excuses. Normandy's on the most important mission there is. They have months to get gear to the ship, or at least to issue Shepard an expense account. Instead, they trickle in a few credits after each mission.