I urge you to start exploring RAW processing ASAP: the amount of additional information you have to work with is considerable and a lot can be accomplished with a processing engine like Lightroom (which I wholeheartedly recommend).
THIS. I second this ten hundred percents! XD Really, though, RAW offers a whole lot more flexibility while not detracting from the image's quality. You may have to buy an external HD, though...
On to my critiquing... keep in mind, this is all my own $0.02, with my own biases and partialities. Also subject to my laptop's screen calibration, which may be off... again...
To me, it seems a large chunk of the above shots are overexposed. In the shots with the flowering ice plants, the flowers (the most interesting part of the shots) are blown out or near-blown out. In the shots with the crashing waves, the frothy water (the most energetic parts of the shots) suffer the same thing. In the shot below the crab, the pathway (the "artsy" part of the shot)... you get the point. Admittedly, some of these are very difficult to capture properly given the range you need to capture in the same shot... dark rocks with VERY bright water, etc. Additionally, it's probably largely your lighting's fault; shooting in full, direct sun produces some extremely difficult scenarios. As Whimgrinder noted, overcast is wonderful for photography. And as others have noted, filters and polarizers can work wonders.
Aside from exposure, I encourage you to play with composition. Many (most?) of your shots are pretty well-centered. I'm sure you learned all about the rule of thirds in your class, and I find that, typically (NOT always), shots that follow that rule are more interesting, more visually pleasing than centered shots. For the sake of example, your lighthouse shot and the meerkats. In my very humble opinion, the lighthouse would have been much more interesting if it were a third from the left of the frame instead of centered. I say the left, specifically, because the little building in front of it is off-center, giving it a right-weighted appearance; so, framing it on the left sort of balances it, despite it being off-center. Since I can't see what's the the right of the frame, for all I know there was a huge, hideous abandoned warehouse or something there that would have ruined the shot had you off-centered it to the left, in which case centering is fine. One note about using the rule of thirds with animals in general, including bugs and such: frame it so that the subject is facing INTO the frame, not out of it. When framed such that the subject is facing the edge of the frame, it creates the feeling that the subject is going to run into a wall or out of the image, which kind of tends to create a sense of tension. When framed so that it is facing INTO the frame, it makes it feel more like the subject wants to be there, or is behaving more naturally, as opposed to making the viewer feel like the subject is trying to run away from having its picture taken.
The meerkat shot is the perfect example of when NOT to use the rule of thirds. In my opinion, that is far and away the best shot shown here and is very nearly perfect. But to focus on composition, the reason this shot is perfectly suited to being centered is because of the "weights" of the two meerkats. One is taller and narrower, the other shorter and wider. They're perfectly balanced just as is, yet they're different
, creating interest. You also caught the perfect pose. One is looking directly into the camera, seemingly keeping an eye on you and their audience, while the other watches over its shoulder: the shot captures the nature of the animals perfectly. Absolutely wonderful shot.
Regarding software: I, personally, use Photoshop, but Lightroom is also perfectly fine. I've just been using Photoshop for probably over a decade, so I'm more comfortable using it. Also, since you're planning on playing around with focus stacking, I assume you're not afraid of using some of the "new-school" techniques available and, as such, recommend you also look into HDR. I've JUST started playing with it, but it's a blast. The range it allows you to capture in a single final image is incredible. Some of those over-exposed shots could have been absolutely stellar as an HDR, I suspect.
Think that's all I have for now, lol... take it all with a grain of salt.
Oh yeah, and your dog is gorgeous. I can't believe how similar my mutt looks to your purebread, even down to the eye color. My girl clearly has white German in her, lol... Fantastic dogs, no? ^.^
EDIT: In my experience, built-in color effects (such as your camera's "Vivid" ) are crap, and I stay as far away from them as possible. I ALWAYS aim for the truest color balance, and if I want to emphasize something later on, it can be done in post-processing.