I have been through Don Jones course and have been working with Tom Alexander for several years now. The core of Tom Alexander's methodology is based on the work of Don Jones. I think you pretty much nailed in the "cons" of Don Jones. The core of what he is presenting is solid but a lot of the software and such is pretty dated but the price is very reasonable. Tom uses CQG and a few of the traders do as well. Quite a few others use Market Delta and other use Investor RT. I personally use Investor RT and use a combination of market profile, bar charts and candlestick charts. I don't use the footprint chart but some of the other traders do use the footprint--personal preference.
I have found the educational service and support provided by Alexander Trading to be high quality. I have subscribed to other educational services in the past and learned a few things but mostly lost money. The core of AMT as taught by Tom is really similar to Don Jones just more robust and up to date. I use the methodology for a combination of day and swing trading where others use it more strictly for day trading and still others use with option strategies.
The "con" to Alexander trading is that it does take awhile to really grasp the AMT and use it to trade well (that is probably true of any methodology). You are not buying some indicators and waiting for them to give you a signal you are trying to gain a better understanding of the movement of the markets and that does take awhile.