...usually 3.5" External Drives have power supplies with them and for the same rotational speed they perform better than the 2.5" External drive equivalents... plus usually you can get a 1TB drive for the price of a 500 GB portable now and more storage is better
But I think in this kind of situation the performance bottleneck is coming from the wireless connection and not the hard disk. Perhaps if you're connected via ethernet you might notice a difference but if you're accessing the drive wirelessly then the difference between 2.5 and 3.5 isn't going to matter?