CI v2.1.2 to v3.1.5 Upgrade Problems

I think the migration guide is thorough and clear. I did migrations with some assisting tools:

1) If you are on Window , get something like Windiff or similar then compare the two directories say CI_old and Ci_new or whatever you want to call them
Or if you are on Linux or Mac then 'meld' is an alternative for Windeiff
By doing comparison on directories , the tool will point out the differences between old and new

2) You then can merge them together by carefully selecting the legacy codes you want to keep on Ci_new

3) At the end of process , then you can do SVN add /commit depends on the changes you made
OR git add / commit

Those are approaches I employed to successful migration. As Kaosweaver said, I found the changes in class names are much annoyed but you dont have other options
I built little script in perl so it go and check class name in Controlllers / Models / Libraries and made the changes with little effort

Good luck