There are a number of factors to consider - the bottom line being that only you can decide what you want. Some of the things to consider are:
What brand is being used in your area so that if you run into problems you can call on some local experts. This includes what system is your club using (if you belong to a club) and what is your local hobby shop stocking in case you need some after-sales service.
You've encountered one of the basic rules of DCC - is the system that you're going to purchase upgradeable so that you don't lose all of your investment. Decoders are compatible with any type of system. However, the command stations, throttles, are not necessarily compatible with other systems, or even within the manufacturer's own suite of systems. In the case of Digitrax, the throttles, command stations, throttle plug-ins, are all compatible within the suite offered by Digitrax. For example, I can plug my UT1, UT4, DT100, DT300, DT400 throttle into a Zephyr, a DB150 Empire Builder command station, or a DCS100 Chief command station. Or, if I have a DB150 command station and I want to move over to the Zephyr, I can use the DB150 as a booster. And all of my LocoNet wiring with the throttle jacks all around the layout can be used on any of the Zephyr, the DB150 or the DCS100 command station. Can the system that you are looking at do this?
And of course, the final consideration is the budget. What can you afford? And it you can afford it, always go for the system with the most bells and whistles. If you purchase a lower-level system, you will soon be wishing you had purchased the higher level system. For some basic rules of DCC, look at the lower part of this page on my website.
http://www.railwaybob.com/Modules/WhatIsDCC/DCCWhatIs02.htm
In my case, because I belong to Ottawa Valley HOTRAK which uses the Digitrax system exclusively, and because Digitrax is very popular in Ottawa, and because my local hobby shops carry Digitrax, and because I know a bunch of guys who are Digitrax experts, my system is Digitrax. This doesn't mean to say that your choice will also be Digitrax.
Have fun. (I am!)
Bob M.