MCSE certs prepare you for a vastly different job than IT Support. Think CompTIA A+. IT Support and systems administration are different jobs and different certifications help out in different ways.
When I got my CompTIA Security+ in college, I got asked by interviewers why I got that and not the CISSP. The answer is, while the CISSP is a far more respected certification, the requirements and entry price are also far different. The CISSP is not an entry-level certification, it actually mandates a certain number of years in the industry.
MTA is entry-level. MCSA is entry level. MCSE is for established professionals, it is an expert-level certification, so of course it's more respected. The people taking it are already well-respected experts themselves.
The MTA is the Microsoft certification that's most comparable to this. Not MCSE.