Warning: spoilers for the Deus Ex series contained within, read with caution.
Both Deus Ex: Invisible War and Human Revolution are obvious candidates for this editorial series, both games feature their own obvious design flaws that have been flogged to death in critical circles. This is especially glaring considering the praise heaped upon the original of the series. However, there are a few more subtle insidious mistakes that are worth digging in to.
The real issue with these games, in my mind, is not late development cycle console ports or outsourced boss fights - it's that both games try to use the original as a template without fully grasping what made it all work.
In Deus Ex the player is introduced to his colleagues at U.N.A.T.C.O., then given a chance to get to know each of them develop an understanding of each character. Then the game pulls the rug out from under players' feet, revealing each of them to have their own agenda within the bigger conspiracy that drives the plot of the game. JC Denton spends a few hours with these characters, working a few missions with each of them - learning to loathe the characters that come back as boss encounters and appreciate the agent who becomes your ally against the Illuminati. Invisible War and Human Revolution introduce you to a bunch of characters in the opening half hour and then expects you to care after a conversation. At least IW keeps these characters around as the face for each of the game's factions. They don't have a lot of personality, per se, but at least there's the player/quest-giving NPC bond there. In HR's case, no one I know who has played the game cares about Megan. It's the characters in your earpiece throughout the game that resonate. The bad guys do not matter to the player, the scientists and wife the main character is trying to rescue do not matter to the player, but when your chopper pilot gets shot down and surrounded by baddies I abandoned any pretense of a stealth run to rescue her.
The real root problem I have with both follow-ups to the original Deus Ex is that they all share the same setting. Not just because any sequel has to meet the bar set by the original, but the nature of the conspiracy-thriller plot. In DE the player was sent on a series of missions as part of a counter-terrorist force only to discover that both their own organization, as well as the groups you acting against were all being manipulated by one grand conspiracy toward their own nefarious ends. The next two games put the main character (and thus the player) through the same plot beats. The exact same ones. Players are expected to wait for the characters to catch up to their personal knowledge of the setting, this is incredibly frustrating. Neither game does much to help this matter, in Invisible War it seems like everything Alex D learns about the secrets of the setting comes from the same characters that did the revealing the first time around. Meanwhile, Human Revolution will use its prequel powers to include specific elements from the first game, like F.E.M.A., without ever elaborating on anything. Players see pieces, but no one ever sees the whole puzzle. HR is at its very best when it has nothing to do with the first game. Running around doing side-missions in Hengsha felt like the blend noir and cyberpunk the series always wanted to have, I wish the conflicts surrounding augmentation technology and its implications had been the entire plot rather than the cat's paw of Bob Page and his omniscient council of vagueness.
A better option might be to take a page from Bioshock. The second game took players to the same setting and was less for it, but the next iteration is taking the formula of retro-futurism, crazy powers and criticism of a philosophical movement into a new context and looks much better for it. This same idea could serve Deus Ex; applying the storytelling and style of gameplay to new conspiracies. Imagine running around as cyborg Freemason agent, infiltrating the halls of power or wielding high-tech weapons against futuristic Teutonic Knights.
I don't hate either Deus Ex sequel, I probably give Invisible War more credit than it deserves. However there are more interesting ways to comment on the games' flaws than going back to the same old saws critics have been using. I doubt any follow-up to the franchise could live up to the original in the eyes of fans, simply because of its iconic status, but treading over the same ground is not the way to go about it. New designers need to take the ideas of Deus Ex into new directions if they have any chance of meeting the fans' standards.