This method is not recommended but it works. Im not responsible for any loss of data or issues that you may get from using this method.
This a look at this:
http://steamcommunity.com/profiles/76561197960506479/screenshot/597000291566469453
Proof that the 10 mod limitation can easily be bypassed and it only took me 10-15 minutes to figure out how, which means that if i can do it so can you!
1)Download all the mods you want to use from the steam workshop and run the game once to launch the modmanager and updating all the mods to its latest and greatest.
2)Start sorting out the your mod list 10 mods at a time starting with those most important and in the correct load order and save the lists on your desktop like List1, list2, list3 and so on where list 1 is represents those mods that are highest on the load priority list. When done close the modmanager without starting the game.
3a)Open all the lists you have saved in wordpad or similar program(one that keeps the formatting), also open modlauncher.sch located "C:\Users\xxxx\Documents\My Games\runic games\torchlight 2". Inside modlauncher.sch it will look something like this:
[MODS]
<INTEGER64>MODGUID:137438746
<INTEGER64>MODGUID:136196864
<INTEGER64>MODGUID:137336889
<INTEGER64>MODGUID:136192903
[/mods]
3b) Keep the [Mods] and [/mods] but delete whats inbetween and copy & paste the data from your list1, list2 and list3 where list1 should be placed at the top followed by list2 and then list3. Save and close the document. You can open the modmanager again by launching the game from steam to see if they are all on the list and you should be able to fix priorities as well but you cant launch the game due to the limit.
4)Launching the game. Once you have your list in order and are happy with it close the modmanager if its open and go to the "\Steam\SteamApps\common\Torchlight II" folder. Rename(DO NOT DELETE) modlauncher.exe to modlauncher_bak.exe(if you cant see the .exe it means you dont have extensions view on, just rename it to modlauncher_bak). Make a Copy of Torchlight2.exe and rename the copy Modlauncher.exe(or just modlauncher if you cant see extensions).
5)Last Step. Create a shortcut to torchlight2.exe on your desktop. Right click it and choose properties. Add "MODSCHEME=MODLAUNCHER.SCH" without quotations to the target line after whats there. Should look something like this "C:\Games\Steam\SteamApps\common\Torchlight II\Torchlight2.exe" MODSCHEME=MODLAUNCHER.SCH . Press apply and OK. Now use that shortcut when you want to play TL2 without mod limitations.
Enjoy.