I'd like to start out with a question. If you want something, does that mean that getting it is a good idea, and that you'll be happy with it? You can take a few minutes to think about that, but the answer you'll probably get is no. There are some cases when getting that thing has more complexities than it seems, and with those factored in, you wouldn't think it's a good idea after all. Other times, you don't know what you're asking for as well as you think you do, and it turns out that it would be bad.
Playing through these cases, there's the very distinct sense throughout that this series is very much based on things you wanted that didn't really turn out to be good ideas.
I want to start with the basic premise of the case. Maya Fey quits Kurain to be a defense attorney and work with Phoenix and Apollo, with Pearl, the new Master, as her assistant and Edgeworth as her friend and mentor. You obviously like this idea, but how is this going to work? Being familiar with the characters, there are a few questions that come up almost immediately. How can a character like Maya be a lawyer while retaining her personality, which includes a lighthearted lack of forethought, common sense, and practicality? Those traits are contradictory. Unsurprisingly, this theoretical design problem creates a practical playability problem, in that Maya feels extremely out of character the entire time. When you have a markedly out of character protagonist, the player will easily get distracted. You had this idea, but the idea itself proved to be a problem. You have other problems. How are the other characters going to react to Maya being a defense attorney? Well, I can't see the characters coming to terms with it quickly, so when they do in-game, it's out of character and thus distracting. Come to think of it, most of the canon characters are out-of-character. Adrian Andrews most certainly is.
Before continuing, there are some critical side points to address. I extremely highly recommend that you not do as many of your own sprites. Yellowcab's sprite and the sprite of the case 1 killer are both unpleasant to look at due to the relative sizes of their head and neck. Also, swearing in cases is a reportable offense and can get your cases taken down, so please remove most of the profanities. "Ass" and "bastard," I believe, are fine in moderation, but the others are not.
Looking at the custom characters you have, most of them seem 2-dimensional. They lack backstories and personalities besides one or two distinguishing features. Zuma is the girl who is singing along to her iPod too much. Yellowcab is the sweaty guy. Case 1 killer is a stereotypical American west rancher. Case 2 killer is the obnoxious guy who swears a lot and comes up with excuses. Case 2 defendant says "sheila" a lot. Phoenix's defendant in case 2 is a rude person. For these last four, I'm not saying their names because I don't remember them. Your custom characters lack personality, and that is greatly weighing down your stories.
Even the plot isn't conducive to what you're trying to do because it doesn't make much sense due to plot holes and poor pacing. Why is Edgeworth on the ceiling of a disco club in the introduction? Why exactly is Maya leaving Kurain? Doing it to avoid conflict between her and Pearl is far too flimsy a motive, especially if they have no relationship afterwards. Most of the conclusions in the investigation segment are illogical. How does Maya have the money to get an apartment? How does Maya get into law school? Why is Trucy on trial? What was the point of the investigation sequence with the tree? A lot of pacing is also bad. For instance, well, quite often. This is egregious in the prologue, with incessant time skips, and the investigations of case two, where illogical deductions are made and facts come out of nowhere. For instance, the connections between the three cases, the hostage situation, and most everything with the taxi systems.
The crime and investigations were also lacking. The investigations were horribly, horribly linear and I needed a walkthrough for most of them. The logic function was poorly explained and poorly done, in particular. A lot of the logic bits didn't flow. Anything requiring evidence was a good example of this, and so was the needle and hole. The relevance of the two hasn't been established, and in hindsight, why would the needle have even been thrown away? Most examinable objects were far too small to catch. As for the crimes, they lacked a certain Ace Attorney flair. I'm still trying to work out the timeline of events in case one, so I can't comment on that, but the idea that three criminals with the exact same M.O struck at the same time by sheer coincidence is absolutely ridiculous.
Lastly, the logic. This is really bad. The logic chess made no sense whatsoever. What did Flip have to do with anything, what was the importance of the motive, and... Well, the second round just confused me. As for the psyche-locks most of them were off. I don't see why the key couldn't have been simply stolen, and Taxicab's sweating hardly proves he was nervous about the conversation. A massive number of contradictions weren't even contradictions, either. Contradictions should either disprove the witness' statement or (in rare cases) answer the witness' question. Most of your contradictions weren't either. Other times were logic problems. For instance, Racinder may have said he couldn't give the killer an alibi, but a witness said he could. It also isn't quite reasonable to assume the killer works for the company based solely on the M.O, because the technology might be common, or the culprit could work for the manufacturer. The timeframes for the alibis weren't established. The bumper also doesn't show car damage was impossible. I'm still lost on the purpose of the clock...
I hate to be negative. I mean, I really don't want to be negative. To be perfectly honest, everything you've made so far needs massive overhauls. It can be done, but not without a massive amount of work. So far, you've just put in things you like without regard for how they work as a whole. I want you to make the best case you can, and in order to do that, you're going to have to think a lot more about design.