This seems to be a common misconception. Just because you install using Softaculous does not mean you have to use the Softaculous updater. In the case of WordPress, or any other system that has an inbuilt updater, you'd be crazy not to use that rather than Softaculous's.
Secondly, many of these web applications don't have auto-update systems at all - Joomla itself didn't until very recently. If Softaculous etc provide something that's 100 times better than running old unpatched applications.
Neither of these are reasons not to use fantastico or softaculous; just don't use their update systems unless there's not one provided by your application.
Third, I have a client who demanded a Joomla installation. As you know, Joomla requires a significant amount of processing which makes it a terrible program to use on a shared server. To satisfy my client, I found WebHostingBuzz's "specialist hosting" which offers a Joomla-tailored (among others) account. My client is happy which makes me happy - particularly as there has yet to be a problem after a couple of years. WMB has servers in the US and Europe so be sure to link to the location serving your target audience.
Joomla, properly set up, is not particularly resource hungry. If you have been using hosting that has problems with it, you've been using poor quality hosting. Perhaps strong words, but this has been borne out by years of hosting Joomla sites with no problems. No doubt there are resource intensive components/modules, but that's not directly Joomla's problem. It should be no more resource heavy than WordPress.
Back to the original question - Softaculous appears cheaper, has more scripts, and is more regularly updated. Fantastico appears to have been largely deserted by it's owner, so I'd say its day is gone. Softaculous is also getting a lot of recommendations. You left out Installatrong, which is about half the price of Fantastico (Softaculous is about 1/4 the price). Installatron is also good, but has less scripts. I think on balance I'd use Softaculous.