First: yes, this feels like a student production, because it's made under basically the same circumstances: getting who can be got for free, but doing the best they can with what they got.
STAR TREK PHASE II clearly aims to be the fourth season of the beloved-but-canceled show. The YT broadcasts make this clear by subtitling this inaugural episode "4x01". STAR TREK CONTINUES accepts that and takes the fifth season. Between the 'real' Star Trek (TOS) and these two fan-made productions, something like the promised "five-year" mission is finally fulfilled.
"In Harm's Way" does a pretty good job of tying together several already-established ideas and situations -- utilizing no less than five TOS episodes for direct plot, another for character details, and even .... well, let's just say there's clearly awareness of TNG and at least one of the movies. All of this is well-tied together -- and if any of it seems gratuitous, it's in a spirit of fun that can be shared by the viewer.
Given a pro team of cast and crew, this would have made a pretty strong episode. Instead, we have a volunteer team, operating on a student budget. Does it show? OMG yes, of course it does. Does it suffer? Well, ten minutes of setting up plot can seem a lot longer when you're wondering if it will all be worth it. But then BarBara Luna shows up, lighting up the screen, William Windom hits his cameo with grace and gravitas, and the episode never leaves you wondering again.
There's more than that: the CGI is a little ambitious but I say "good on ya mate" -- it adds interesting visual life to a by-now engaging story. Malachi Throne has an awesome cameo later on, but by then we're sold: the episode works well enough to carry the viewer past the remaining rough spots. Which is to say, the show as a whole is more convincing than the individual cast members or production qualities (the lighting being particularly wanting, which just highlights how important ST:TOS's lighting was). No doubt these details will improve in future episodes, and I look forward to seeing the actors grow more into their roles.
Oh -- and I must second the other reviewer's praise of Kurt Carley as Pike. He has his own spin on it, and it's a good one. More than once in this episode, he delivers some simple mundane line and makes it sound just exactly right. Glad I'm seeing this -- 17 years after it was made.