Back in 2018 I decided I wanted a manual E91 330i with the N52 engine as a daily, but they were nearly twice the price of a 325i so I bought a 325i with 132K miles but full BMWSH for just under £3K. I had the inevitable electric water pump failure at 135K but no other issues in the 7,000 miles I did with it. But it just felt a bit sluggish, so getting back up to speed on a Motorway on any sort of incline meant changing down to 4th. I think the problem was pairing an engine that revved to 7,000rom with excessively high gearing, so 70mph was only 2,500rpm in 6th.
Anyway after a year I tried again and had the same problem with 330i prices being so high. So I talked myself into a manual E90 330i instead as I found one with the split/fold rear seat option, also N52 engine, and it works much better and it's very refined for long Motorway trips which is largely why 5 years and 17K miles later I still have it.

Although it became a Cat N last year.
Although I do now wonder if maybe a 130i might have been a better idea! Although I found with my 123d years ago the rear is a bit tight on legroom.
I wanted to stick to N52 engines after having had two in my first E86s as they seem to have fewer problems than the later DI N53 engine, and AFAIK all early E9* 3 Series had the N52.
I've no idea about rear space in an E92, but before my Touring I had an E46 325ti Compact that had enough space in the back, it was just awkward getting in and out as my mates were getting older like me!
I can't help with the Skoda although I think you need a better diagnosis of the engine problem.