Yes, no surprise that some older Mac apps will not work under 10.12. That said, Mac apps install differently than Windows applications and at least are easier to move by simply copying them in many cases.
As to drives, my 27" iMac is a Mid-2010. I recently installed a nice "half-terabyte" SSD as the primary and reformatted the original 1TB platter as an auxiliary onboard drive for photo storage. (in addition to my externals) The work was easy and even with that age, the interface was "current" outside of a slightly lower transfer speed. I have 16gb of RAM in it, runs the latest OS, is fast enough to do even the photo processing in Lightroom and Photoshop that I handle a few times a week and and other than a little slight fading of the backlight on the right side of the screen, it runs like it's brand new. I plan on getting at least another year out of it, assuming the display hangs in there. Oh, and I run Win10 in Parallels for support of Quicken. (The Mac version still isn't up to snuff...)
But that's getting away from what I think the OP intended for this thread...there are ways to get what you have on the old over onto the new and it may be worth considering utilities that are geared to do that rather than having to completely reinstall and rebuild manually.
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The most expensive tool is the one you buy "cheaply" and often...