PC Gamer's Dan Stapleton has a short editorial on the "looks like a mod" complaint for sequels that keep significant assets from the original, using Fallout: New Vegas to Fallout 3, Fallout 2 to Fallout, and Knights of the Old Republic II to I as examples.
To use classic examples, Fallout 2 did it right by adding an entirely new story, a new map, new weapons and armor, new enemies, and UI improvements to the engine of Fallout 1. Star Wars: Knights of The Old Republic II The Sith Lords was doing really well by adding a new story and characters, new planets, new weapons and armor, etc, right up until the disastrous ending. Playing these games is a different experience from their predecessors, even though they're similar in gameplay and appearance. They're new adventures.
By contrast, X-COM: Terror From The Deep did it wrong by simply re-skinning and renaming everything with a cheesy underwater theme, (just a handful of aliens and techs didn't have direct equivalents in the first game) and adding only a few UI improvements and the dreaded two-stage terror missions and alien base attacks. It really was the same game with a different look, and that wasn't different enough to call it a new game.