The whole of Jurassic Park was designed to be a safari-like experience, and that means taking people around really big wildlife areas to reach attractions. Both the Aviary and the Jungle River Cruise wouldn't be reacheable via the Park Drive for sure, even though neither of them were built at the time.
And this is based on what evidence exactly, some well made but still unofficial fan maps and the non-canon Telltale game (apart from Troodon being venomous)?
What’s not to say that the River Adventure and Aviary would have been reachable on foot and within the resort? Neither the film, novel and other material have confirmed or denied both this. Your statement appears to be based on nothing more than hearsay.
And paleobotany doesn't really add much, as it was implemented in-game. Not to mention that it would have forced us to get a second DLC to unlock it (in case you were planning to involve Dr. Sattler, which would be required, as I take RtJP's campaign is completely separate from the rest of the game).
On the contrary, Paleobotany does add to the game; it provides another way to increase the rating and lifespan for the dinosaurs. In a way it can be considered a more cost effective way of improving the herbivores' rating than via the Creation Lab, especially if players are running low on money to create new dinosaurs.
And as SotF wrote in an earlier post, Dr. Sattler examined a
“species of Veriforman that has been extinct since the Cretaceous period”; which confirms that not only InGen has recreated the dinosaurs but also prehistoric plant life as well. Thus Paleobotany in the Jurassic Park era of the game makes sense both logically and lore-wise.
As for your concern about it would have forced you and other players to purchase Claire’s Sanctuary as well, it’s baseless. If it were implemented, the Paleobotany system could be unlocked in a similar way to Proceratosaurus and Dryosaurus; if you purchased the DLC, you would unlock and be able research it at a certain point in the Return to Jurassic Park campaign. If you hadn’t purchased the DLC, it would remain locked and you would be unable to use it.
Whereas transport wouldn't have screwed up the schedule so much and would have helped retain further depth.
Personally speaking, I find the removal of transport management within the Jurassic Park era and the greater emphasis on dinosaur visibility to be one of the biggest highlights of the DLC. We no longer have to worry about placing countless stations that suck away a sizeable chunk of precious power just to satisfy some remarkably lazy guests. I believe putting it back in would once again make Park building a chore.
Building monorail stations, especially on both Isla Muerta maps and Isla Pena, is a rather joyless and time consuming chore. It takes a lot of hard work to find the right place to build the track/station and have it blend in with the landscape, but at least it is possible to make it look decent by having it blend with the landscape of both the island and the park, and the track can be placed over buildings and paths.
Those advantages won’t be available with the Park Tour, the latter is impossible, and the former would make building the park more of a long drawn out task and have it look cluttered and unaesthetically pleasing, e.g. Multiple stations in the resort alone. Thus you would get all of the drawbacks and none of the benefits from the current transportation management.