I can completely understand that personal standpoint. As a matter of fact, I kind of feel the same way (particularly with the Gym sets), but the success of Neo Destiny indicates that the community as a whole doesn’t feel that way.
Trainer specific pokemon are my personal favourite.
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There are no “rookie” cards in the set.
This is definitely a valid argument, but the fact that this is where Dark cards were introduced mitigates that a bit.
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Indeed, it is part of a paradigm shift which adds to the story.
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You can put any card in a “ROOKIE” top loader. lol
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Team rocket pop rate for psa 10 1st edition are quite high (mostly 150+ except for a few). Same things goes with both gym sets but to a lesser degree.
This contributes to the lower price point.
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Non-holo versions of holo cards were also a problem.
If Rocket had retained 1st Ed. Dark Charizard as a holographic-only card it would be far rarer and far more valuable. As it stands, the market is diluted with dozens of non-holo versions of the card/artwork which makes it far less special and therefore less desirable. Blaine’s Charizard from Gym2 has kept up with and often exceeded Dark Charizard in price, despite being printed later and long after the original Pokemania of '99 was dying down.
It’s definitely not undervalued, but the potential is indeed there.
Not every set is equal. At least with Pokemon, each one has good value. If we compare with sports or MTG etc… this hobby is doing great. There’s booster boxes from 20 years ago selling for a couple hundred or less from these other hobbies.
Even something like Base 2 is outpacing anything else released that year.
I used to think like OP, but then I checked my Magic cards which are 4-5 years older than Pokemon and my rares or foils are mostly worth less than $1. 
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TR wasn’t a very popular set for the Pokemon league. You had to have another “Dark” pokemon to have yours evolve. At first it was cool looking cards with the sinister darkness around it. But most players got discouraged having to change all their cards when a older “Haymaker” deck was still dominating. Most people traded the TR cards away.
As far as collecting, they don’t have the same appeal as the older sets. Back in Y2K erra the Charizard base was all everyone wanted. It wasn’t until NEO came out that people started to get interested in the cards again. But by then most of the kids (and parents) grew tired of having to buy cards that no one desired.
Simple: it didn’t have a dark green toad thing.
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Poor Dark V had to wait.
It is true that all the dark cards were too weak for competitive play apart from Dark Vileplume, but Rocket also had some good trainer cards that changed things up a bit. At least compared to fossil it was a better set, since fossil only had Ditto and Magmar, and a couple of borderline useful cards like Muk and Articuno, which kept things stale. Ironically, the best packs to buy for League play at that time were base set 2 packs, so I am not sure playability has much do to with current prices. Personally, I think Dark Charizard, Dark Blastoise and Dark Raichu all are more iconic and have more collector appeal than any holo from Jungle or Fossil.
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While I completely understand that not all sets are equal, something just triggers in my mind when I see WOTC 1st Edition holos listed for under $50 (or even $100). I know I keep harping on that point, but it just does not feel right seeing a PSA 10 WOTC 1st Edition holo going for $40-50, regardless of the fact that it’s Weezing, Arbok, Hypno or Slowbro.
I just kind of feel like growth is inevitable. Not saying it will become Base, Jungle or Fossil, but I certainly think that in 3-5 years, those cards will be worth more than their current price points.
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I agree thats it’s undervalued. That first ever secret rare Dark Raichu might be one of my favorite cards off all time. Who remembers the confusion about the set number back in the day. lol
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For the longest time I thought people were straight up lying when they talked about Dark Raichu. I was certain it did not exist because it was not included in the set list with the other holo rares. It blew my mind when I saw one in person for the first time. The confusion continued when the Japanese Dark Raichu showed up with the Neo Discovery symbol and a white star. 
Couldn’t you then say the same thing about Jungle and Fossil? Non-holo versions of holos don’t seem to be bringing their values down much.
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They’re much harder to grade, but you bring a fair point.
I think the hobby will mature in years to come. We’re at a point where some 10s barely earn more than a weighed booster pack. I agree that doesn’t make much sense.
If some of you spot a few anomalies or strongly feel certain product is undervalued, then why not put some money into it and prove us wrong 5 years from now? 
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Not to mention that the artwork for the Rocket set is just PHENOMENAL. The coloration on some of those holo patterns is beautiful!
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For me the Team Rocket set is my first exit of Pokemon. Stores barely had it in stock. I remember it being released just before summer vacations and after the summer the fakes were going haywire with all kids coming back from Spain, Italy and Turkey. Fake, non foil, Dark Raichu’s were everywhere and I remember everybody complaining about the tons of trainer cards they got from the packs. And I think for many the Team Rocket set connects directly to their first bad experience with Pokemon (either due the fakes or availability) and thus lost it’s grace.