Water line sizing to shower/tub
There is no benefit to "downsizing" the supply size; however, with tub fillers it usually is not a deal breaker because it just takes a bit longer to fill up the tub. If you look at the size of the tub filler spout, it may be no more of a restriction than you already have.

Both the stop valves and the threaded adapters that are screwed into your cast brass tub valve arms are available for 1/2" O.D. tubing (1/2" compression). Stop valves for 1/2" compression may be difficult (not impossible) to find in a "straight" configuration (as opposed to an angled 90° configuration), I would suggest that is the reason the plumber used 3/8" tubing and fittings. 

How will an aesthetically pleasing shower mixer arrangement be created for this? I recommend that you consider changing the filler valve to a faucet set that has a shower diverter incorporated, there are many available styles: