I) Make wine bottles take up 4 slots (2x2) of inventory space (not due to their size in themselves, but because they take a lot of care to pack, envelop in straw etc.)
II) Make them larger content-wise, say 1.8 l instead of 0.6
III) Make them cost more to make (6 or 8 glass instead of 4)
IV) Make the bottle rack be 6x6 (or maybe larger, e.g. 12x6 [would need new graphics

Why:
1) There is currently NO reason to build Bottle Racks (yes, they cost less, but not if you count cost per stored bottle, or if storage space is sparse enough to be valuable) instead of Chests. Other than looks, of course, they really look neat and diversity is allways good. With these changes the bottle racks will have at least the same storage cap as the chests, being cheaper and more beautiful, but lacking in versatility.
If a player needs a wine cellar, he will (probably) build bottle racks, else he will build chests.
The changes in mechanics will be that storage of bottles will be harder in any container or inventory not a bottle rack, which in my eyes seems appropriate.
2) You need a booming 166,6 bottles to save the contents of one full barrel of wine (this may be intentional and wanted, in which case II), III) and 2) can be discarded, but) IMHO the wine bottles are impractically small, for production, tapping, trade, storage and consumption.