While I agree with @geraltitude's comment - most likely these games didn't live up to their potential due to budget, deadline or other constraints, rather than the developers idling their thumbs - two games instantly come to mind for me as games that have a whole lot of promise, but which fall short due to issues that could possibly have been fixed had the developers had more time to finish the games. These games are Jeff Wayne's The War of the Worlds (the PC game, not the PS1 one) from 1998, and 7th Legion from 1997.
The War of the Worlds is essentially a prototype of the Total War model - the turn based RISK style world map with territories to conquer or defend, and a real time large scale battle mode to decide who wins the skirmishes in these territories. It's all presented with remixes of Jeff Wayne's fantastic 70's rock musical and an art style based on the booklet paintings from the album. The premise is just fantastic (based on H.G. Wells' 1898 novel of course), with 19th century humans attempting to defend against an Martian invasion, using the technology of the day (while attempting to capture and reverse engineer the alien technology). Sadly the game's multiplayer mode was disabled on launch, supposedly to be patched in later, which never happened, and was riddled with bugs, making several unit types unusable and some maps pretty much unwinnable.
7th Legion was a RTS/CCG hybrid, something we've started seeing a number of in recent years, but to my knowledge hadn't previously been done in 1997. In many ways it looked like C&C, with a pretty obvious aesthetic inspiration from Warhammer 40000, you had C&C style MCV's to establish your base, and WH40K style space marines, mechs and tanks to fight each other with, and of course the five cards that were handed out to each player at the start of the match, which could do anything from giving you a money boost, make a unit temporarily invulnerable or destroy every single building on the map (including your own). The game also didn't use the by that point standardized resource gathering mechanic, instead you were given a set amount of money every minute, and got bonuses for every enemy you killed.
So, yeah, the cards weren't balanced super well, but the game's biggest shortcoming - especially when you consider what genre the game belonged to - was that the game didn't handle the actual mouse recognition particularly well. Selection boxes could only be drawn from left to right, from the top to the bottom. If you tried from right to left, the units wouldn't be selected. Moving units around wasn't too great either, the game was pretty particular about exactly where on an enemy unit you should click to order an attack, it also had a contextual menu that was supposed to appear if you held down the button for a second, but which most of the time appeared instantly and thus cancelled the orders you tried to assign. The pathfinding could've been better too.