A combination of a lot of things.
For starters, the thing is architected poorly, so that does play a big factor in it. I know, I know, it's always the new guy inheriting an existing system that lays to claim that the inherited thing is a piece of garbage, but in this case it is undeniably true. And I can tell you, as someone who has been doing .NET consulting for the last 8+ years, it's not uncommon for MS based solutions to be architected this poorly, but I'll get to the reasoning behind that later.
So yes, poor architecture, lazy design choices (the wrong kind of lazy) but what is most aggravating are two other factors: cost and maintenance. Of course the very first thing I did when I settled in as the new CTO was to figure out how the thing was maintained and how much the thing was costing us a day to run. At my former CTO gig, massify.com, one of my proudest achievements was getting the daily cost of running the site below the price of a pack of cigarettes. Now we are talking about a user generated video content site with not exactly insignificant amounts of traffic and some very healthy storage requirements. When we started out, it was running us around $300 to $400 a day, but by the time I left, it was about $8 bucks give or take. And during the three years I was there, the site never came down unless we took it down for some kind of database migration or similar updating. And all of this happens thanks to OSS software and the ease of use of unix.
Now we are in a situation where we are paying for the server OS's, the SQL server instances and a variety of other utilities to keep things running. Not to mention the yearly MSDN subscriptions. That shit is expensive.
But what is worse is that it's such a pain in the ass to update and work on. Remote Desktop is retarded, but I have no choice as command line maintenance is simply gag inducing. Something that would take me mere minutes in a linux command line takes me an hour or more clicking around like an idiot in remote desktop. Good luck remotely admin'ing a windows server taking a massive CPU load. Now when I was at Massify, I could maintain and monitor our whole fleet of servers from my phone - and on a couple of occasions even did so while sitting through the previews at a movie theater. Do that on MS? MMM ... no.
But back to bad architecture and why it's endemic in the MS development world. ASP.NET. ASP.NET is such a convoluted, poorly conceived, poorly executed pile of shit. THIS IS COMING FROM SOMEONE THAT USED TO SING ITS PRAISES. And when ASP.NET is a cornerstone of .NET development, I don't think it's implausible to rationalize the rampant bad development practices of your typical MS developer back to it and other MS technologies similar to it (I'm looking at you Sharepoint). You see, MS is chock full of shitty architecture. And MS devs learn from MS. It's a cycle of shit that is constantly perpetuated by each release of some new MS technology. And I can tell you, I've seen it time and time again - working for companies like Pfizer, R/GA, some of the top 5 interactive ad agencies, etc. Finding a great MS developer is like finding a great PHP developer. They exist, but are such a minority as to be almost mythical. We used to joke that MCSD stood for Microsoft Certified Shitty Developer. Well, we always pitched it as a joke anyways, in case anyone ever overheard.
So, now we are currently wiping the slate clean and moving the whole thing to an OSS stack. And so far, even in the rough beta stages, we've already demonstrated how superior that whole ecosystem is to where it was before. It's very satisfying to show our licensing agents our new shiny search system (using a heavily modified Solr) and watching their eyes light up as we do things with it that the old MS based search engine simply could never do.
So that's my rant about that. MS is dying shit as far as I'm concerned, only used by people who are somehow locked into it, or are the bad kind of lazy and don't want to challenge themselves. I know that's not very objective, but it's the lessons I've learned.
PS. When I was interviewing with the company, I literally had a 4 hour conversation with the outgoing CTO about the benefits of MVC. He couldn't see them and I couldn't explain it to him in a way he understood. He kept pointing at ASP.NET user controls and how great they were. Of course, several months later I find a page on the admin site that is roughly 26K lines of code in the codebehind with a nice spaghetti mixture of HTML and SQL and C# code. I nearly quit when I saw it.