It's hard to say – Apple doesn't like to discuss those kind of specifications. Flash memory is definitely getting faster, but it does depend on the controller.
If you had, for example, 64 GB of data you'd like to load on your shiny new 128 GB phone, it would take about 18 minutes to upload it at ideal USB 2.0 speeds (probably a bit more, considering the overhead), and a little less than 2 minutes at USB 3.0 speed.
USB 3.1 is also on its way – Apple might skip 3.0 and go directly to 3.1 speed, which is double 3.0's (under 1 minute for 64 GB). It would be a bit of a marketing coup. Thunderbolt 3 is also a possibility farther down the road.
People can only stand to have so many ports on their computers (using the MacBook Pro as an example), so Apple might reduce the number of ports by 1 (eliminate HDMI) first, leaving only USB and Thunderbolt, then bring it down to one kind (e.g., Thunderbolt and use adapters for the rest), and eventually none (all wireless, including charging and headphones). The only people left using cables might be power users with Mac Pros – it certainly would be consistent with Apple's minimalist design ethos.
You can bet they'll advertise it when it happens – I think most people have become accustomed to waiting that chunk of time for the initial load, syncing, and backup, but it will make a bigger difference as media files and apps grow. Wired I/O probably isn't their main priority, since the "average" user may be expected to keep things synced over 802.11ac wi-fi or the new "150" Mpbs LTE.