You won't be losing as many lines as you might think. The 1080 is interlaced meaning you are only seeing 540 lines each interlaced field. The 720 is progressive which equals 720 lines every frame (no fields with progressive).
Make your decision on the progressive versus interlace aesthetics, basically if you want "live television look" shoot 1080 interlaced, if you want a "filmic look" shoot 720p especially as your HD200UB is capable of 60p.
I normally bring everything from tape in as Apple Pro Res, or material from from Firestore DR HD100 I convert to Pro Res straight away. This gives a smoother workflow throughout the whole process especially if you intend using Color and Motion.
Once in ProRes the worflow is smooth through all the Final Studio Apps. Generally I use Compressor but I you need to consider your final output format.
It's difficult to give advice without more specific details and many others more experienced than I can help over on the Final Cut Forum.
Working with such a heavily compressed original format such as HDV can produce great results but it requires care throughout the process.
I and many others have discovered slightly different workflows for different input / output formats can preserve the quality in the end result.