Sorry to hear that. The previous shoulder strap design could fit a 300 - 400 mL bottle but only if it was very tall/slim because the max diameter was 1.75 - 2". I've been looking at these pockets a lot and I think that for almost everything else the side access is better because it is more secure (no chance of a phone falling out) and lets you use the pockets for smaller stuff that would be very hard to dig out from the top (chapstick, sunscreen, car keys etc). So I find the side access useful for a lot of things, whereas the only thing the top access did better was hold really tall objects. The previous design did have it both ways, but having the top access limited how good the side access could be, because to make the side access optimal it needs a more complicated shape (e.g pleating). So I decided to omit the top access in exchange for improved side access, and added this side access to both shoulder straps.
You may still be able to put a water bottle in there because now the side accessed pocket is pleated and larger (e.g. greater girth) compared to what was possible when the top access existed. Instead of putting a tall/skinny bottle in the top, you may be able to put a more normal shaped 300 - 400 ml bottle in the side zipper. Either way though it's going to be limited to quite small bottles where I expect most people will prefer the side pockets. If you want to drink from water bottles with a straw (as some runners do) then the side access obviously won't work, but it is more secure whereas top access bottles can fly out when someone stumbles. To be clear, I haven't tried the newer design with water bottles yet so I'm not sure to what extent they will fit, but overall the side access pockets are much improved and more useful in the newer design.