I don't think this is as big a deal as you're making it out to be. Maybe I'm just used to it, but this is one area where I consider the C89 way to be better on stylistic grounds. (I wrote about this on a stack exchange site some time ago: http://programmers.stackexchange.com/questions/75039/why-dec...)
Realistically I don't think C99 is all that revolutionary, and the fact is there are plenty of people writing C89 in 2013. Let's look at some things C99 adds over C89:
* Mixed declarations and code
IMO not a huge deal, for reasons I give above.
* VLAs
A nice feature, but people have been using malloc for similar purposes for ages, so it's hard to say it's any better than "nice to have". I'd also argue that something that leads me to potentially consume arbitrary amounts of stack space based on runtime decisions is probably not universally good, and I'm pretty cautious about using VLAs even when given the choice.
* Last field of a struct can be variable sized array, eg. struct foo { int num_data; int data[]; };
I like this pattern and have used it a lot. Including with VC++ by having a zero-sized array at the end of the struct. This is once place where I use an ifdef to bridge the gaps because recently I noticed LLVM started doing weird things for this if you don't do it the "legit" C99 way.
* Cosmetic issues like // comments
VC++ already supports this in C89 files as a non-portable extension.
* Portable typedefs like uint32_t, etc.
These are also pretty handy. But if you're building with VC++ you're probably using the non-portable Microsoft ones anyway. (I think VC++ 2010 added the C99 versions too.)
* bool type
Again, every platform and even reasonably sized library works around this with a typedef and some macros.
* Slightly different behaviors for some libc functions
I notice this most for snprintf, where the pre-C99 return value [followed by Microsoft] means something different [and better] in C99. Again there are non-portable solutions for this that you can use ifdefs for.
* Named initializers for struct members
Cool feature. I'd hardly say I couldn't live without it, though. The only place I've really seen it used extensively is in the Linux kernel.
* Stuff that no one uses, such as "static" as used in these slides, or complex numbers, or whatever.
Not a problem since these don't see wide use.