The first wish has to be a reworked Finder app. Although Finder was just rewritten in Snow Leopard for Cocoa and 64-bit support, it has slowly became more and more problematic and performs poorer version by version (maybe beside Mavericks) within the previous 5 years.
It now has awkwardly-laggy scrolling, half-baked CoverFlow appearance and a bunch of performance issues.
It would be really nice to see a revamp of Finder app, maybe taking cues from iOS but still offers the advanced features we now know and love. Maybe like Logic Pro X where certain functionalities can be enabled on demand? Just enabling syncing in Finder is not enough, adding more extension points to Finder would also be really nice. Imagine being able to QuickLook non-standard videos with 3rd party codecs, quickly view thumbnails of non-standard image formats, or do a fast file comparison right within Finder. If this happens, sandboxing will be a issue though and Apple needs to sort that out.
From what we already know, every image processing feature in Photos app is actually integrated with the mechanism of extensions. So it would also really make more sense to bring extensibility to Photos for OS X. This would bring feature parity to Photos app for iOS and help professional photographers better organize and enhance their shots.
In current versions of OS X, filesystem shown in Finder differs from ones shown in dialog boxes, (from Mail app, for example). It would be nice to be able to see all photos within Photos library, music within iTunes library and videos created by iMovie right in Finder.
Maybe Apple should also tweak UI elements a bit. The disjointed arrows should be jointed. Maybe San Francisco can be tweaked and brought to OS X. It would also be nice to improve UI font choice for Asian languages. Many HongKong and Taiwan users have been long complaining about STHeiTi TC, which is designed by mainland Chinese designers who knows little about traditional Chinese typography.
Oh, and please fix the Finder full-screen background black-out glitch. The Image Capture and performance monitor scrolling issue. Various memory leaks. Interference caused by poorly implemented Wi-Fi direct drivers.
And a new filesystem.. Maybe in OS X 10.12 or 10.13 or OS XI?