Is that normal, forcing me to pick and choose, or is something wrong?

I never used Steamworks for mods for Skyrim and only used it for Torchlight II and for that game the limit was 50 downloaded.

Only thing wrong I can see is a failure to use http://www.nexusmods.com/skyrim/? instead. They have a better selection of mods. You have more control over the mods and when you update them, and The Nexus is better run than Steam is. Also with http://www.nexusmods.com/skyrim/mods/modmanager/?, http://www.nexusmods.com/skyrim/mods/1334/?, and http://www.nexusmods.com/skyrim/mods/1840/?, your game will thank you.

I'm not saying that Steamworks is a poor choice, however, I am saying that The Nexus is a better choice in terms of mod availability, moderation, and removal of potentially stolen content from the site.

If it will only check and update 50, then I'll just unsubscribe the mods that don't need updates and favorite them so I can find them later, then it'll load up the other mods. Exploit the limits!