I have a pair of 2015 SEs, a manual and DSG (his and hers). The manual was bought used with 40K in 7/17, the DSG as a leftover in 4/17. A notable difference to me over a pre2015 aside from the engine improvements already mentioned is the Gen 3 extended emissions warranty. 11yrs from original sale date or 162K miles on all things emissions, fuel pump, turbo and so on.
I did just have the DEF supply line replaced on the 2015 manual @ 57K, its VIN was in suspect range. The dealer so far has taken care of it free of charge. I noticed the issue doing a routine oil change. Nothing else to complain about aside from both have squeeky driver windows.
Had an 09 DSG prior - the MKV was an awesome car, but I could not refuse the buyback - and got the 2015 DSG to replace it. My wife still says she preferred the 09 over the 15, mainly for her belief the 09 had more "gitty up". The 15 DSG does have better economy mpg over the 09 DSG (pre fix), something like 42mpg vs 45mpg avg so far (real calc) The 2015 mpg meter is way off in both manual and DSG.
I absolutely enjoy my manual 15 SE which made a fine replacement for my 2000 MKIV 5 sp manual. The 15 is just slightly lower economy so far compared to the '00 manual. The 15 is more powerful for sure, but not by as much as the numbers might make you think.
since you list an 04 manual in your signature- I'll also share how I find myself shifting between 4th and 5th alot (around town) where '00 would be perfectly happy to hold 5th gear. And on the hiway, much under 60mph and a downshift down to 5th may be needed when real acceleration is desired. Despite that - I'll take the manual everyday I can!