When deciding on Megaquirt, or commercially available units, you need to decide if fixing it yourself is OK. Commercially units have a warranty, and support. The MS support community is quite good (actually better than most manufacturers), but when it breaks, you have to fix it. If you purchase a pre-built unit from one of the builders out there, they will typically fix a unit for a fee. If you start experimenting with some of the other features in MS (Extra code), you are on your own for the most part (except for sites like this).
There are a number of aftermaket units out there that are great. They all have hundreds of features and capabilities. Enough to make your head spin at least a couple times.
I like MS for it's simplicity. If everything is wired right, most new installs fire up right away. MT is an easy to use software package that let's you make changes in real time while the engine is running. There are still commercial units out there that can't do this. There are bugs, and untested features in MS (not that there aren't bugs in commercial units).
Yea, MS doesn't do sequential fuel or ignition, but for 95% of all applications, it is not needed.
Again, the decision is if you want a company backing up your investment or not.