It always puzzles me when I read about Czech Pils, for instance, being hoppy. I suspect it is, is just that noble hops are much more subtle than modern "hoppy" American hops.
Maybe there is a degree of recalibrating your preconceptions required? I suppose you could go easier on the hoppy hops, but then would you get the same (or the required) bitterness? I dunno...
(FWIW I used Crystal hops in my pseudo Helles which was great - but in fairness, crystal isn't really an in your face hoppy hop)
It's the less hoppy lagers I find more challenging, Märzen, Helles, Vienna Lager etc... I guess in the UK we're just not really accustomed to these less bitter/less hoppy lagers...
By the way, I bottle all my beers - it may have taken time but eventually they've all come good in the end. So I don't think there's anything per se wrong with bottling lagers - however, it may well just be one of those styles (ha ha - like there's only one lager style!) that is somehow mystically better suited to kegs. Who knows...