The phrase "including X" means that X is not a comprehensive list of effects.
The only way for Suggestion to not be stopped by Protection from Evil would be for Suggestion to not qualify as an attempt to "exercise mental control over the creature." I doubt such an interpretation exists.
For what it's worth, I believe the reference to charms, and compulsions that grant ongoing control is an intensifier clarifying that Protection from Evil will suppress spells that have already been cast on the target but are still in effect. The examples given (Charms and Compulsions) both fall into the category of long-term mental manipulation.
It is likely that at some point play testers were confused about the interaction between spells like Dominate or Charm Person and Protection From Evil, so they added an aside to address them. Asides like that aren't meant to be all-encompassing, they're simply a way of saying "yes, even these."
Appendix: English Fun Time
As with many bits of rules text, this can be interpreted several ways. The way I'm interpreting it is simply the one that strikes me as following the written text most closely, while leaving a minimum of unknowns.
There are other interpretations that are valid from an English syntax point of view, but generally leave lingering questions. Whether these interpretations are better, worse, valid, or invalid doesn't concern me here. Only whether my interpretation fits the printed text.
Okay, so let's strip down Protection From Evil to a more streamlined version that's a bit easier to talk about:
This spell blocks any attempt to exercise mental control over the target, including effects that grant the caster ongoing control over the subject. The protection suppresses the effect for the duration of the Protection From Evil effect.
I've italicized the controversial bit. The phrase "exercise mental control" isn't defined in the game, so you have to pick an interpretation. There are three reasonable ones:
An attempt to exercise control is an action that imposes a condition on a target that forces it to act in a certain way. E.g. casting the Dominate Person spell.
An attempt to exercise control is an action that gives a target a new compulsion. E.g. issuing a command via Dominate Person.
An attempt to exercise control is anything that overrides the will of a target.
You can take your pick. The first one causes the "but what's this clause for?" problem, but both of the second two line up.
For my part, I choose the third interpretation, because it feels closer to natural language, and I don't like adding rules constructs without purpose.
Let's look at an example. Say I give you a Suggestion, and order you to dig ditches until the spell ends (in 10 hours). Three hours later, the English sentence "I am exercising mental control over you" is a valid statement. Even though I'm not actively issuing new commands.
Now suppose someone casts Protection From Evil on you (and we suppose it works the way I say it does).
The English sentence "I am attempting to exercise mental control over you, but it is being suppressed by Protection From Evil" is a valid sentence, that is in agreement with the text of the spell.