I actually can't get too worked up about the issue of in-house movements. What counts for me is how well it keeps time and how rugged it is. Most of my watches don't even have display backs.
Start with the actual design process. The tiny independant is probably going to do some basic calculations for the overall power flow etc so but there's some serious maths involved and I doubt they actually calculate many things. The large manufacturer has a team of specialist designers with specialised CAD tools. I'm not sure which is better/worse - an artisan using a mixture of experience and trial and error, or a team of engineers taking the last femto-erg into account.
The same goes for manufacturing. What's better - loving, intensive hand finishing or souless precision maching? Neither guarantees accuracy or reliability.
As for innivation, I'd put it into two categories: true innovation, which for me implies thought and understanding (the best examples being the new escapements) and "toys" made possible by CAD/CAM and spark erosion. The human dimension is important for me, and something that's only possible because of modern design tools lacks something.
If being in-house is really important, then clocks are where it's at. Top-end, and even mid-range, clocks are nearly always artisan-designed and totally hand made. Given that there isn't the constraint of fitting everything into a tiny space the designer can make design choices that allow for an optimum balance between function and appearance. There's also plenty of scope for originality and innovation. Finishing is generally meticulous but not fussy or decorative (simple understated elegance in most cases). The materials used are normally traditional and simple. As they're primarily timekeepers and not fashion items that double as tinekeepers, the performance is exemplary. There's ooddles of contact with the maker, individual whims are the norm and they're as custom as you can afford.
nick