Warp speeds, traversable distances, stardates, the 'uniqueness' of AI, what Klingons look like, what Trill look like, whether Trill can be transported or not, when cloaking devices were invented, the 'uniqueness' of Q, when the prime directive really does or doesn't apply, whether there actually is or isn't money and what exactly that means, etc, etc, etc...
The list could probably go on for pages.
So on the "it's always been a total mess" side we have:
Warp speeds, which had different scales and evolved with technology
distances, which the writers got confused about cause they didn't think they'd have to check every previous distance mentioned
stardates, which could have simply changed along with galactic distances, communication, and new cultures joining the Federation
AI, which can simply exist in many different forms
Klingons, whose genetic problems were explained in dedicated episodes
Trill, who are a strong example for messy continuity
cloaking devices, which also evolved with detection technology
Q, who can simply have similar counterparts like Trelane, just like there are also multiple shapeshifting species
prime directive, which evolved over time and depended on each Captain's interpretation weighing the whole situation
money, which is the second good example for messy continuity.
On the "continuity depends on canon and has been pretty good in TNG-VOY" side, we have:
Vulcans and Romulans always had single-pointed ears and green blood, Klingons always were fierce warriors, Romulans always were related to Vulcans, the Borg always had implants and cables, the Enterprise 1701 pre-refit had the same look inside and out, 2260s equipment and uniforms kept the same designs, warp speeds had the same scale, people's names were consistent, LCARS looked consistent, sounds were consistent, the Ferengi always had round big ears, Romulan ships were green and bird-like, Klingon ships were green, Borg ships had geometric shapes and no outer hulls, the Borg were a collective, deck numbers stayed the same until Nemesis, the galactic map stayed consistent with the quadrants and where the galactic powers had their regions, past events were referenced consistently, weapons had consistent looks and sounds, uniforms followed consistent patterns,...
Now imagine all of these examples hadn't been consistent. Then it would be a real mess. Would you still enjoy it as much?