I'm going to jump in here. I want it noted that my opinion is from a user's perspective. I'm taking my moderator hat off for a minute.
I use MakeMKV to make all of my non-3D backups. I've been doing this for MANY years at this point. I ALWAYS use it with AnyDVD enabled, ignoring the MakeMKV warning about incompatibilities. Never had a problem there. MakeMKV is convenient, but, IMO lacking in several key areas that I think CloneBD can eventually bring to the table.
The first is handling screen pass protected titles. Let's be honest, it's a real pain in the ass to have to track down the proper titleset. However, as mentioned, I use MakeMKV with AnyDVD, so, this is only an annoyance more than a problem since AnyDVD will give me the proper title.
The second is handling episode BD's. They don't always author the discs in nice neat orderly playlists. You have to determine what playlist corresponds to what episode. There are a myriad of ways to do this, none of them automated. CloneBD should be able to help with that.
The third is not something I personally care about, but, has to be mentioned anyway as some WILL care. That is compression. Some people want to keep the HD audio, forced subs (we'll talk about this one in a minute), and maybe shrink the video down a few gigs to save some space. I think that's a reasonable "ask". CloneBD can do this. Mostly. It needs a bit of time to mature (again, we'll chat on this in a sec) but it's got a lot going for it.
Finally, obviously, Cinavia. I'm going to take a contrarian argument on this one. Since the topic here is MKV, honestly, I couldn't care less about Cinavia. And until a solution provides me with 100% lossless HD audio in that department, Cinavia removal just doesn't work for me. I sincerely applaud the effort and for those that care about Cinavia, this is a great option.
So where does CloneBD currently fall down?
The most obvious is the fact that all video is transcoded currently. There are technical reasons for this that as a developer can be appreciated, as an end user maybe less so. All I'm going to say on this one is I get why it's being done and respect their decision to force it for now. I'm not going to debate anyone on this topic or explain it. The simple fact is, transcoding is enabled for all operations right now and it's done intentionally with good reason. Eventually, once CloneBD matures, this will not be the case. We'll leave it at that.
I'd argue that subtitles are a shortcoming right now, as well. MakeMKV has a brilliant feature to not just keep subs based on user preferences (albeit complicated for end users in some ways to get the preferences string set correctly to auto-select what you want...still, it's powerful nonetheless) but they can also scan for forced subs while its at it and create a separate sub track for forced subs and flag it. We need this option. Period.
So, passthrough of video (we'll get there, I'm quite sure), passthrough of audio, passthrough of subs with the ability to create separate forced sub tracks, and the ability of auto-selecting based on my preferences (english audio, hd, english subs as an example)...that will make it surpass MakeMKV because of the additional episode disc handling and aforementioned screen pass annoyances. Let's be very clear here, this is not a difficult thing for them to do. However, it's also not their top priority so this is going to take a while to get. Right now they're rightly focused on the transcoding engine as that's the real power behind CloneBD. They're likely working on improving Cinavia. And they're working on titles that simply don't work for whatever reason. Honestly, those are the right priorities for them to work on. The "easy" things like proper MKV support, it'll come, but, not right now. I can promise you I'm in the same camp as you waiting for it. As an end user, it's my most wanted feature and I'm as impatient as everyone else. In the meantime, I'll continue to use what works for me....which is MakeMKV. I keep checking out the new CloneBD builds as they come to see if we've gotten closer to the ideal outlined above. I don't have any unreal expectations about getting my needs met soon. I'll continue doing what I'm doing....using what works, checking on each new build to see what's improved, and providing feedback when I can to help the developers improve CloneBD little by little.
If you're not comfortable with where CloneBD is at and don't want to buy something based on promises, I can respect that. To you, I'd said, sit back and wait and watch those release notes for each new build. Eventually you're going to see the MKV output get some love. When it does, then let the real comparisons happen. It's just not ready.....yet.