My old rig is still working great but her days are numbered. Started looking at replacement options and was surprised to see the all-in-one's which do not have optical disk drives. Is that because optical disks are considered obsolete? I guess you would need an external USB device for optical disks? For my purposes I will probably get another tower as my monitor is a nice Asus only about one year old and I can not see paying almost 2 grand for an all-in-one. However, the all-in-ones are very sleek looking which is especially appealing to my wife. Optical drives are certainly dying out, I honestly can't think of the last time I actually NEEDED one.  The thing with optical drives is that they are physically large so take up SPACE inside the machine, by removing them it allows the machine to be made smaller or to fit more useful components in the space that it saves.  If you do still need one then yeah, just get a USB drive, they are fairly cheap.

All-in-ones are very nice and compact but they aren't really as upgradable, think of them like a laptop in that respect, you can upgrade the RAM, storage and sometimes the CPU but not really much beyond that.  Of course it is up to you if this matters to you.As Camerongray said Optical Drives are starting to be phased out as something found on all computers. It's very much similar to how Floppy Drives used to be included on all PCs, but then people realized that they were seldom used and manufacturers decided they could trim costs by not including them.

If you have Discs you need to use, There are as you noted USB Devices available for that. My new Thinkpad T550 doesn't have an Optical Drive, for example, but I was able to install a few programs from DVD discs using a USB DVD Drive. The "preferred" approach is to use a USB Flash Drive; Windows and most other Operating Systems can now be installed via a Flash Drive.

With an All-in-one you are paying for all the added bits and bobs such as the screen and so forth. I think I agree with your sentiment that a new tower would make more sense, since you've got all the other bits and bobs. It would also end up quite a bit cheaper. You can get a reasonably CAPABLE system for around 500 dollars or so.

Another consideration is that your current system may just need a "REFRESH", (depending on it's age, of course). The most common reason a system starts to "die" or become unreliable is typically when the Hard Disk starts to fail, or of course from malware or other nasties or just accumulated cruft from years of use, and installing/uninstalling programs, and so forth.

Oftentimes a new Hard Drive with a fresh OS install can seem to give a system a second life. Depending on the age of the system a bit of extra MEMORY can help as well. And that can often be a lot cheaper than a new computer, so it may be worth investigating as an option.

Not that I don't like the new computer smell myself Thanks. Yes, I just did a refresh last year...new HD, new graphics card, triple RAM (1->3 GB) and new disk drive along with a new monitor, wireless mouse and a fresh Win 7 install. I am really happy with how well it is running but it is getting close to 7-8 years old.IMHO, anybody who has a limited budget should think about a partial upgrade and not a full replacement of a working desktop.

Now and in the future ones must get Apps from an on-line App store. But if you are content with what you have, thee is little reason to change.
The notable exceptions are new things that just were not available before.  I found an App that I must have and it only works with Windows 8 on a Desktop. So I wail have to someday pay for Windows 8, which comes with almost all new desktops.