I have not played either, however there is a thread on RPG.net that discusses many of the same things: The RPG.NET thread on the topic
However, on reading it only the first comment is useful to you, so I am going to quote the relevant parts here:
Troubleshooters is the 25th Anniversary edition of the Mongoose 2004 PARANOIA rulebook (formerly known as XP). There are minor tweaks to the rules, but it is basically the same game. Likewise, the companion Internal Security rulebook uses the same system, though there is extensive new material there for BLUE-Clearance IntSec missions. Neither is mechanically complex, and both place unique emphasis on the Gamemaster's supremacy. Every rule in both books exists as a non-mandatory advisory to the GM's incontrovertible authority.
In contrast, High Programmers is a completely different game with an unusual and innovative rules system. It isn't necessarily complex, but the players have more options and hence a greater cognitive load than in Troubleshooters or IntSec.
Each book offers copious advice on designing missions, plus pregenerated player characters. Troubleshooters, in particular, adapts the XP GM Screen's "mission blender," a collection of tables that lets you generate an entire mission randomly with the roll of a mere five dozen or so d20s. Troubleshooters also includes Ken Rolston's classic introductory PARANOIA mission "Robot Imana-665-C" as well as a fine new mission by Gareth Hanrahan, "The Quantum Traitor." High Programmers includes one mission, "Disaster Management."
— Allen Varney, 04-16-2010
Other comments in that thread indicate that the Official Paranoia Development Blog has information on the designers goals with each system.
I hope this helps, it seemed a shame to have this thread with no answers for so long.