Originally Posted by
jsdavis
Accoriding to Shimano diagram, you can mix and match all the R3030 and 3503 drive stuff. However the shifter and FD should be from the same series if running double crank.
2016-2017 SHIMANO Product Information Web
If I'm reading that right, the only things that are cross-compatible are the triple shifters and triple FD's (and cranks, but that's kind of assumed). You can't mix and match any 2x9 shifters/FD's, as you say. But, critically, you also can't mix any of the RD's.
On the plus side, it seems like the new RD's support a much wider cassette range than most old-school road RDs, making the loss of cross compatibility with Deore less painful.
EDIT: Oops, I may have read the chart wrong, and jsdavis is correct. It looks like, at least for 2x9 groups, the R3000 and R3500 RDs are compatible, with some slight differences in max cog size.