I'd characterise myself as a software engineer (mostly parallel Fortran these days) with a reasonable amount (5 years) of experience with Matlab. Coming from software engineering I think the major deficiences you will encounter are:
Matlab doesn't have very well developed facilities for structuring large software systems. If you are an adherent of OO then recent versions of Matlab might appeal, there are now OO facilities within Matlab, you no longer have to call out to Java (or have Java call Matlab). I haven't got deeply into Matlab OO yet, I'm not sure it answers any problems I have so I can't comment on them other than to say that they look like a late addition to me. Which, of course, they are.
As a development platform Matlab is
deficient in comparison with the
kind of facilities that IDEs such as
Visual Studio or Eclipse have. The
editor is OK as an editor, but it
doesn't provide much help when
refactoring. There's no integrated
source-code control, nothing like a
project browser, not much in the way
of intelligent code completion and
the like. As a Fortran programmer
the lack of these doesn't bother me at all :-) but
more sophisticated developers might
miss some of it.
I find Matlab's data structures (not just the ones they call structures, but all of them) a bit clunky. In particular you have to go to OO to do dynamic data structures. I guess dynamic data structures are outside the core of what most Matlab developers work with, but as a software engineer you may miss them.
As @disown has already pointed out, deployment is a bit of a mess too.
Having said all there are signs that Matlab is becoming more suitable for use in a production environment and getting away from being strictly for prototyping or small-scale development by non-developers. For example, the Parallel Computing Toolbox is, I think, a very good implementation of a system which does for parallel Fortran what Matlab originally did for Fortran. Sure, it can be expensive to deploy Matlab on a cluster but that's only money.
As to the point about Matlab being proprietary, and therefore closed. It's not something that bothers us tremendously from day to day. If The Mathworks collapsed tomorrow, and I don't suppose it will, we could continue to run Matlab for a couple of years while we lined up a replacement. And I'm sure that if the Mathworks did collapse then there would be a rush of companies bidding to sell us a replacement.