The main thing is to make sure you have a high flow waste, (they often come with one included anyway it seems) and that the waste pipe is properly installed so that it drains quickly. Any shower tray needs to drain properly, but I guess with a low profile tray there is less scope for error.
(we have a standard tray at the mo and doesn't drain at all properly cos of the length and poor installation of the waste pipe).
Other than that I think it's then down to personal aesthetics and preference. We are putting a low profile tray in our new bathroom refurb as it will be used with a 3 sided enclosure so it's visually quite obvious in the room, and low profile one will look better. If it was going in a corner then it wouldn't matter so much. Though my Dad will prefer it as well as he has reduced mobility and finds it much easier to get into a shower when there isn't much of a step up.