Taking a step back, I have a few questions to ask before making suggestions. For fun I do a lot of builds and assessments of potential builds for coworkers and have found that the best way to avoid small regrets/compromises that crop up 6 months post-build is to ask a lot of questions before the process starts:
- What programming needs does your wife have? Is she SSHing/remoting into another machine? Is she doing something ridiculously RAM intensive like building custom Android images locally? Does she have multiple 1TB files in her codebase or anything else like that?
- Do you have space concerns?
- Do you have noise concerns? If so, are you open to modding?
- What size/resolution monitor are you using?
- Is there a particular space the computer needs to integrated well into? Are there furniture or decorations you want it to match/blend well with?
- Is the case going to be wedged in a corner, up against a wall, or have any other ventilation restrictions?
- Music/movies only? You certain you'll never game outside of RTSes? Which RTSes do you play? Do you play them competitively? Will you ever want to max them out graphically?
- For movies, are you doing anything intensive? Are you a stickler for the best scaling and need madVR Jinc 3+AR / Lanczos3+AR?
- Do you have a separate NAS solution? Do you need redundancy for data stored on the machine?
- Are you planning on suspending the mechanical drives or considering other options to eliminate drive vibration?
- I'm assuming you're not going to tinker like crazy to try to get the best overclocks, etc down the line?
- How long are you planning on using the system before upgrading?
I don't think it's odd that you're looking at cases you consider to be on the nicer end of things. Once thing I've found consistent for most of the folks I've built for is that solid choices for case and PSU last through many many upgrades (if you choose to go down that rabbit hole), even after the rest of your system is out of date.
A bit of caution: I've done 2 builds in the 350D and one thing I've noticed about the case is the 3.5" drive mounting mechanism is not ideal. Even using the rubber grommets for the drives, fast spinning mechanical drives can cause the drive trays to vibrate against the case. It's possible to suppress but it requires some light modding.
Thanks for the in-depth reply. Let's see:
1) She mostly deals with web development and database design. Nothing too intensive and no gargantuan file sizes. She does remote into her desktop at work quite a bit, though.
2) No real space concerns. It'll be going under a desk, though, so we don't want it to take up too much leg room, which is why I eventually decided on a microATX case. OR, if you meant space INSIDE the case, then no...the 350D should be sufficient.
3) No major noise concerns. The last machine I built was an absolute beast...sounded a bit like an airplane taking off. I can't imagine this being worse than that especially if I go up a step on my psu (looking at the seasonic G360) and without a video card.
4) Monitor is a small Samsumg HDTV/monitor. 24" or so, but I don't remember exactly...1080p.
5) I just wanted a case that looks slick. No worries about matching. I don't think they make cases in cherry wood.

6) It will be about 6 inches away from the wall and under a desk. Should be plenty of airflow, though...no real restrictions there.
7) 99.9% certain about gaming. Starcraft II is the only thing I own right now that I might dust off at some point. I've got a PS3/PS4 and do all of my gaming on there.

I just want good blu-ray playback. I'm not familiar with the terms you mentioned, so...no?
9) My wife uses Carbonite for backup. I have an external drive that I back all my music onto so I can transfer back and forth between work and home. Also use dropbox a fair amount.
10) I just planned on using whatever is built into the 350D for my drives. My current build only has one SSD and one HD.
11) No overclocking. I used to be into it and it's a headache I was happy to be done with.
12) I'd be happy to get 3 years or so out of it. If it's still working well by then that'll be cool. If not, I'll feel like I haven't thrown my money down a drain.
Yes, I would like to use this case again if all goes well. Every review I read of the 350D seems to scream quality and ease of use. Your note about the 3.5" mounting issues are interesting.
Like I said before, I'm not opposed to other cases. I've researched a lot of them. The nanoxia deep silence series. The Define R4 (although I've read of similar issues with MB alignment that others have mentioned). Arc Midi R2. Arc Mini R2. Define Mini. Several Antec cases (Three Hundred Two, etc.). I will say I found the Antec cases to be on the uglier side of things, though.
I also looked into some Bitfenix options.
The 350D is what I came away with. If something changed one day, and I did decide to pursue gaming, it seems well set up for liquid cooling. Alignment of the MB and ease of build don't seem to be an issue. Cooling seems adequate if you aren't using a serious video card. Noise is average.
But anyway...all this to say, if you have something you feel strongly about, I'm happy to reconsider.
Thanks again for the help!