Then they decided to hop on the Java bandwagon, and rewrote their whole UI using some kind of cross-platform Java GUI toolkit. App startup time went from like a tenth of a second to like 30 seconds (at least, that was my subjective impression at the time). Every part of the GUI was laggy and glitchy, it crashed regularly, the documentation was reorganized and much more confusing, etc.
The big-ticket feature additions which supposedly justified the rewrite were some gimmicky stuff for writing formulas in a more standard-math-typography way instead of as plain text, plus some related handwriting recognition thingy, but this ended up being slow, confusing, and ineffective, and cluttering up the rest of the interface.