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It is likely, that my plugins are more complex than other's, because I have to replace & modify many basic functions. Therefore, if new LinksSQL versions are released, I may have a lot work to do the upgrades for the plugin.
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That defeats the purpose of a plugin. Overwriting core code is a bad idea for the people using the plugin and the person making the plugin. What happens if people with to uninstall the plugin. Will they be left with overwritten modules that they can't reverse?

What if your plugin has some bugs that cause errors, people won't know whether it is a links sql bug or a bug with your plugin, GT may start getting support email for bugs that aren't to do with them....I'm sure they'll appreciate that

A plugin should _add_ to what is already there. If you have to modify core code then either you need to re-think your plugin or you are duplicating features as such. The most obvious example is the thing you mentioned above about the add/modify forms....errors are already displayed in a neat and clear fashion, why would you then make a plugin to restructure the form pages so all the tag names are different?....it sounds like a wheel re-invention