Convenience. Security. These are two concepts which are at odds. Maximum convenience means no security. Maximum security means no convenience. Finding the balance that suits your specific needs is up to you.
Also, security is not something you install and forget. Do you think hackers don't try to find new vulnerabilities and new ways to exploit them every day? Well, they do and we have to make changes in our security products to protect you. Otherwise we wouldn't be selling a security product, we'd be snake oil. At the very least that would be immoral.
A quick rundown of your issues:
1. Super user locked out of every account after security logs them as accessing the admin area. This means that your sessions expire too soon. This is fixable in Joomla's Global Configuration. You could also remote the Administrator Secret URL Parameter feature but you should enable the administrator secret URL parameter. Or enable none and let two factor authentication protect you (that's why I contributed that feature to Joomla back in 2012). This is something I have said since 2010, when Admin Tools was launched. You have options, use the ones which make sense to you. Defaults are just that: what I believe are good default values if you don't know what you're doing and want to start somewhere.
2. Emails for every admin action, every admin uses on all 14 domains. Whenever we create a new feature we always consider very carefully its pros vs its cons. In this case, you receive an email when your site's Global Configuration is changed or Super Users are created outside of the backend Users manager. Both of these events are anomalous on most sites (and for those sites they are not they are an indication you're doing something ill-advised or outright detrimental to your security). That's why these two features come enabled by default: they notify you of anomalies. Unless, of course, you are talking about security exceptions. In this case it means that you never took the time to configure Admin Tools, which is a security tool, not something that you install and magically makes your site secure. There is no such magic solution. If there was I'd be selling it for 40 million Euros a year to companies and governments and they'd buy it without blinking an eye because it'd save them operating expenses more than ten times that price.
3. Media players stopped working because of MIME issue which never happened in the past. There's a reason we had to do this. We did our research and found a security issue in Joomla regarding SWF files. See https://www.nc-lp.com/blog/csrf-token-steal-in-joomla I'm sorry that we inconvenienced you, but I'd posit that a hacked site would be much more inconvenient. Also see #4.
4. PDF component download error which never happened in the past. We fixed a bug which allowed arbitrary access to non-Joomla folders. Considering that the frontend protection is meant to stop that I'd say this is a good thing. For what it's worth, you just need to add the folder in "Frontend directories where file type exceptions are allowed". Adding them to the folders where everything is allowed misses the point of front-end protection (which is the whole point of the .htaccess Maker) so maybe you can just not use the .htaccess Maker on your site? The drawback is that it's easier to get hacked. For example, an upload vulnerability means complete compromise of your site. With .htaccess Maker's front-end protection you are protected even if the attacker uploads a malicious .php file since they can't access it directly. Again, convenience vs security.
5. iFrame for online book reader 404 error which never happened in the past. See #4.
6. Download component does not find new FTP upload items which never happened in the past. See #4. Also note that this is a strong indication that your download component serves files directly from a web accessible directory. Therefore anyone can download any of these files by guessing the filenames (which is typically far easier than it sounds). It sounds like an insecure or at lest not well thought out download component to me. I am not pulling hair from my butt here. I have written Akeeba Release System used for all of our downloads and also the downloads for Joomla! itself. I think I can convincingly claim I know what I'm doing when it comes to download components ;)
7. Cannot login to front end without deleting the .htaccess first. I have no idea why since there is zero usable information in that statement. There are no changes in the .htaccess Maker which could explain it. Please make sure you are using version 5.1.2. The first releases, 5.1.0 and 5.1.1, had a bug with the frontend protection. We pulled them and replaced them as soon as we found out about it, releasing 5.1.2 which fixed the issue.
At the end of the day Admin Tools is a security tool. It can help you set up and maintain total security on your site. It's not a security service that you put in front of your site, never configure, never disturbs your site and rarely stops actual hackers who have a moderate knowledge of what they are doing. Admin Tools takes about 1 to 5 hours for the initial setup and about 1 hour per year per site to maintain. If this is not what you are looking for then yes, Admin Tools Professional is not for you. This is OK. Security tools are not for everybody. Maybe you don't really need total security of the kind you can achieve with Admin Tools. Different sites have different threat models and security needs.
Which brings us to your original question. Yes, you can replace Admin Tools Professional with Admin Tools Core but I see no reason to. You'd lose all features which make Admin Tools useful. At this point you can simply uninstall it. You should also delete the .htaccess files from your site's root and the administrator directory. Joomla still needs a .htaccess so just copy its htaccess.txt into .htaccess in your site's root.
Finally, as a side note, if you want to downgrade your subscription please note that you will lose your renewal discount. It only applies when buying the same subscription (renewal), not when downgrading.
I hope this sincere information helps. I remain for your questions.
Nicholas K. Dionysopoulos
Lead Developer and Director
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