We did the Magical Express and arrived at around midnight and it was a disaster. The service itself was so convenient but just make sure you have all of your toiletries packed in a carry on (they have a restriction of the size of liquids on airlines so we had to put ours in our checked luggage). We had no contact solution, toothpaste, etc. and we were up until 3 AM waiting for our luggage. The front desk didnt even have a complimentary package of contact solution for us to use. :veryconfu The got someone to open the store to get us some, and then they added it to our bill without telling us. The Magical Express is a great service with a major flaw.
Forgive me ... I don't mean to be mean, but the major flaw was in your planning and preparation, not in Disney's Magical Express.
You knew about the restrictions on toiletries. You could have purchased and packed toiletries of acceptable sizes, and brought them with you in your carry-ons.
You knew that DME luggage gets delivered about 3 hours after you arrive at your resort -- it says so right in the DME booklet that Disney sends you.
So if you know you can take smaller sized toiletries, and you know you'll be without your luggage until about 3 hours after you arrive, then you need to plan accordingly. Your lack of planning, or of reading the directions (in the DME booklet, Disney even recommends you pack a carry-on for your immediate needs).
If you know what to expect, or if you don't know what to expect because you didn't read the instructions, then how is that a flaw of the system???
Let's say you go to a waitress-service restaurant. Let's say you have 3 very hungry and rambunctious kids. You walk in and discover you must wait for a table ... then once you are seated you discover you must wait to get menus ... then once you get menus you discover must wait for the waitress to take your order ... then once you give your order you discover you must wait for the food to be prepared and for the waitress to bring it to you ... and so on. After the meal, you might think that the food was great but the restaurant had a major flaw because of all the waiting, and your kids were hungry and unhappy and caused you difficulty during all that waiting.
Well, of course the restaurant had no flaws at all. No one brings starving and unhappy kids into a waitress-service restaurant and then expects to be eating one minute later. You know how that system works, and based on that knowledge you decide if you want to use that restaurant's system. If you do want to use it, you prepare, either by going to the restaurant before the kids are starving, or by tiding them over with a snack before-hand, or by skipping the restaurant entirely and opting for a buffet or fast food.
I hope you can understand my analogy. It sounds like you described DME the way it was designed to operate, and the way that literally millions of us have been very hapy with.
Again, I say this objectively, not with any intent to insult or flame, but honestly, the flaw was with your lack of understanding of how DME works and how to plan accordingly.