Umm, Sirbomber, the old way is still there. The new way is just another option. If you don't like it, use the old way. At worst, you'd have to create a dummy DLL that does nothing to load.
As for why this upgrade was needed, consider this. To make that shortcut, you must specify the path to OP2. Since different people install OP2 in different folders, it means they have to customize the path. This is, in many ways, equivalent to playing with the .ini file. Granted, they do it once, rather than when they want to switch between mods. But, I should point out that the new mod loading system wasn't designed for temporary mods. It was designed for permanent mods, like the net fix. If you want to use a temporary mod, I stronly suggest you use the old method. The benefit of the new mod loading system, is that no end user ever has to play with the mod loading system to get permanent patches to load properly. They can simply be packaged with Outpost 2 in a way that will work no matter where they install it. There is no hardcoded absolute path for them to adjust anywhere. If you'll recall the long set of instructions that were posted on how to get the net fix patch to load in earlier versions of Outpost 2, well, that's exactly why it was designed.
Edit: It's possible that the old way is not entirely there. I may have built the newer version starting with some outdated source code. If that's the case, then certain functionality may have been reverted. I haven't verified this against the older version, but I did notice a size discrepancy, so this is probably the source of the trouble. The change to op2ext.dll was introduced in 1.3.5 Beta 2. If you're having trouble with the /loadmod parameter, then try an earlier version. I'll see if I can obtain a newer copy of the source for the next release.