Well, you can just rip movie only without re-encoding. Clown_BD and tsMuxer have been mentioned already for extracting the movie, and the container to be used depends on your playback device(s). With 1,000 BDs, that's gonna take a whole lot of hard drive space. But if that's what you want to do, it's certainly the simplest method. BTW, that's not "uncompressed"; there's compression alright, you're just *not* re-encoding. BD standard specifies H264 (also called AVC), VC, and MPEG2. MPEG2 was used a good deal early on for re-releases of older movies.
Let me offer another possible method: Quality-based encoding using X264 encoder, and one of the various front-ends for it, viz: Ripbot, Handbrake, et al.
Movie content varies considerably in its compressibility. Clean animation like WALL_E needs much less bitrate than a movie with pronounced grain, like, say, Defiance, or an action movie with a great deal of motion. The maximum allowable video bitrate for Blu-ray (40 Mbit/sec) is massive overkill for a movie like WALL_E. So if you *do* decide to re-encode, using the same target file size is a bad idea. You'll at times use far too much bitrate when it isn't needed, and conversely, some movies may have low bitrate artifacting and posterization/banding. Mind you, H264 degrades rather "gracefully" as you lower the bitrate. You have to go pretty low to get the macroblocking so characteristic of MPEG2. The main thing to look for are a softening of the picture, and then posterization/banding when bitrate gets low enough.
Re-encoding is a fraught issue with some, of course. Any re-encode (even to a higher bitrate) entails quality loss, however slight. If you're going to bother with re-encoding, you should aim for a quality level that satisfies you, viewing the content on your particular display. X264 encoder offers quality based encoding, the quality level being controlled by "CRF" (constant rate factor) values.
A CRF value of 18 should be nearly indistinguishable from the original to most people; higher values yield less quality, and smaller file sizes. I don't find screenshot comparisons to be particularly useful, since one doesn't view a movie as a series of stills. It has its place though for comparison purposes. Again, output size is unpredictable, but you can expect to save a considerable amount of space, at times cutting output size in half. X264 outputs AVC/H264.
Here's what I do:
1) Run a driver-level decrypter like AnyDVDHD or DVDFabPasskey in the background. Either one will remove the encryption on-the-fly, and you can work direct from disc, not having to rip (copy to hard drive) the movie first.
2) Open Ripbot and click add a project. Navigate to the BDMV folder, then STREAM. Select any *.m2ts file and let it analyze the disc. It will automatically select main movie and if it's spanned over multiple *.m2ts files, will join them. Wait for Ripbot to demux the streams to your project folder. Chapter timings will be included. Rarely, copy protection and/or a complex disc structure will prevent Ripbot from correctly joining all the *.m2ts files of main movie. It may occasionally be necessary to extract main movie first with Clown_BD, which invariably does it accurately, in my experience.
3) Select audio encoding. You can copy stream, for example, or use Aften to re-encode to 5.1 AC3 at 640 kbps.
4) Select video encoding. Select a CRF value or type one in. As to level, I use 4.0 for MKVs (see what your playback device wants). Use one of the preset speeds (slower preset yields smaller file output). The default tune is fine, but you can tune for Film, Animation, Grain, etc.
5) In Properties, you can crop and hardcode subtitles. Ripbot is usually accurate in its cropping values, but one should double-check them; also use the preview function. As to hardcoding subtitles, Ripbot will identify any embedded forced subs for you. You can build these into the picture, or the main subtitle track (the first one listed). As to cropping, it's your choice. Black bars don't consume much bitrate.
6) Selectable subtitles, also known as "soft" subs. You can include soft subs as well. (What sub format your playback device supports determines whether you need to convert them first).
7) Select output container, e.g. MKV. Give the project a name and save it. You can load multiple projects into the queue and do them overnight, for example.
8) You can edit the Ripbot config file to keep your preferred default settings.
I play my MKVs direct from external powered hard drives via USB on my LG 65" 65LW6500. I always hardcode any forced subs, but don't bother with selectable subs. My TV only likes *.srt subs, and it's a pain to convert BD *.sup files to *.srt. OCR always has mistakes, so one must edit them. I also need to use AC3 due to my setup. Again, playback device determines what format is required.
Anyway, there's one way. Good luck.