My only issue with Omnibus is if the publisher doesn't put the books in the order they were meant to be read. Many don't even have a table of contents, so it's hard to find the next book. Thanks for the tip. I will learn how to use EpubSplit.

I bought an omnibus edition for my Mom and I have to have it ready for her by February, which is about the time she will have read all the books I put on her Kindle already.
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started showing minor but definite issues about eight or nine books into the omnibus - slightly slower to open
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Annoying but solvable. Make sure that you can find the page that you have ended on. Then quit the book. Delete the book and reinstall. Now find the page that you left. It will work like it did the first time you opened the book.