Handbrake is still actively developed, it hasn't been discontinued. It isn't as good under Windows as it us for OS X as, for OS X, it has access to the QuickTime/AAC encoder which is 1000000 times better than the FAAC encoder it uses for Windows. This is only for encoding audio. Plus, with OS X, Handbrake has been tuned a little so that it takes less time to encode a movie than with Windows. I believe this is due to Handbrake being coded for OS X first and then ported over to Windows.
You're confusing technology a little bit. ISO is not a DVD standard but rather a file that can house all sorts of data. ISO files can represent software, ripped DVDs, etc. An ISO file from a ripped DVD houses all of the audio and video files that a DVD has in a single file. It doesn't convert the DVD (which is already encoded using the mpeg-2 video standard along with AC3/DTS audio) but just takes the video files and places them in an ISO container. That would represent an exact copy of the DVD though. Now, when you take that and convert it using a program, you are further compressing the DVD. Since DVDs are encoded using the mpeg-2 standard, they represent a compressed video. So the videos on DVDs are already compressed, they were sourced from a studio lossless version of a movie (which takes up about 2000 GB of space). When encoding, you are taking that already compressed mpeg-2 video and further compressing it using mpeg-4 AVC. The results are acceptable but the resulting mpeg-4 video, NO MATTER WHAT, will NEVER have the same quality as the source DVD.
mpeg-4 AVC is a better video option when encoding videos from a lossless source. The Blu-ray standard relies on either VC-1 or mpeg-4 AVC h.264 for video encoding from the studio lossless file. On a bitrate-to-bitrate comparison, mpeg-4 AVC is going to outperform mpeg-2. So, theoretically, if you had the 2000GB studio lossless movie file, encoding it to mpeg-4 AVC at a certain bitrate would be better than encoding it using DVD standards at the same bitrate.
That isn't the case here though since DVDs are already compressed. There is absolutely no way you can ever, ever, ever, ever obtain better quality than your source DVDs when you are ripping and encoding them.
I rip my DVDs to a single, lossless file once and then encode them to a single mpeg-4 AVC file. The file is encoded with Handbrake's Apple TV 3 profile. I then take that single mpeg-4 AVC file and watch it on my Apple TV units, iPad, iPhone, MacBook Pro, etc. I don't see a need for encoding multiple versions of the same movie for various devices. I can understand doing this if you are working with a 2000GB studio lossless file but you are working with an already compressed, standard definition (DVDs are not high definition!) video. You might save 100MB by encoding it using a specific iPhone profile but that's about it. My mpeg-4 AVC videos normally take up anywhere between 800MB-1.75GB depending on the length of the movie.