This game has a lot of potential, a lot of it!
For one the story seems like it would be very nice to finish up. The story thus far being an artifact called the Trickhat that can cause a lot of chaos and problems for Merlee's kind. Kind of funny how I thought his grandson was Merlina for a moment (I think that's how her name is spelled, correct me if I'm wrong) until he joked around with his son and song stated that watching the stars was dull. The fact it can block out their ability to see the future is great enough concern to go on a quest for it too. That being said, looking forward to seeing if this game will be finished in the future.
The graphics are nice, however I noticed with some character sprites that there was an outline of gray around the characters. Most notably this applies to Mario and Luigi and becomes obvious when they jump around in their house or outside of battles. Another is the height of the game is around five pixels too long, may want to clip that a bit so there isn't excess at the top of the screen.
Another thing is that while the audio is nice, I feel you could do better than trying to use songs and sounds directly from the game series itself. You should give the Newgrounds Audio Portal a check, not only are there a lot of Super Mario series fan works there but many other songs to choose from that you may find fit the game even better than what you currently have. Noting this seeing as how the first battle using Wario and Waluigi, their song sounds rather grainy and low in quality. That seems to be the only song I notice that needs to be replaced so it doesn't lower the quality and enjoyment of the game.
However, using the voice clips of the various characters I found were alright. You could also check here on Newgrounds in the audio forum for voice actors if you decide you want every dialog box to be voiced by someone.
Which brings me to my next point. While I notice there are some intentional spelling differences, I noticed a few others that make the dialog a bit wonky at times. For instance, Mario ed Luigi instead of Mario and Luigi is a bit awkward to read along with a royal guard before battling Wario, Waluigi, and Popple saying He instead of Here. Could always ask a tester or two to help find spelling errors so the dialog is smoother.
Lastly, I notice the battles are a bit weird. For instance, there is no consequence for running from battles, while it may make some battles later take long to finish, it does not penalize the player in the slightest. Could at least make the player lose a few coins for running. Also if the player does decide to run from battle then the enemy they were meant to face simply disappears meaning you could make the game go a lot faster by simply running away from every battle you can possibly run from.
The battle mechanics were nice but it sucked that Mario and Luigi could not use their hammers to attack and could only defend with them. Maybe look into having a battle option in a later build of this game where the player is given the option of attacking with either the hammer or jumping mechanics. The only problem I had with Wario and Waluigi was throwing Waluigi's bombs was a bit difficult to master seeing as they seemed to want to stick to his hand even when I pressed the jump/throw button for him. The Popple Attack was also a bit difficult to master too.
Overall, this game has a lot of potential in regards to being a completed game; but, in order to do that a lot of things need to be tested over time either by yourself or with help from others (which you can do by uploading this as a project by pressing the "P" button at the top of the page or by uploading it as a dump item by clicking the arrow pointing down at a box) and possibly changing up the audio to make the game even better. Best of luck if you decide to complete this game!