It's certainly unfair to compare the quality of effects in these two films, seeing how An Unexpected Journey has ten years of advancements in digital technology at its disposal (not to mention, a budget 2-3 times larger than Fellowship). However, the same could be said for the comparisons between the original Star Wars films and prequel trilogy; yet, many prefer the SW films that are several decades old now to the comparatively-fresher prequels, purely in terms of effects and action. So why, then, does the first Hobbit movie avoid being branded with the same stigma?
Well, the difference is the SW prequels swap ingenuity for rudimentary filmmaking; scenes are saturated with eye candy, but realized through basic shooting/editing techniques. An Unexpected Journey, by comparison, does not use effects and a bigger budget as a crutch; instead, it combines approaches to create dazzling 3D dioramas and elaborate shots that make diminutive Dwarves and Hobbits appear all the more authentic. Moreover, it does improve the integration (and interaction) of live-action characters and settings with CGI elements - passing over the heightened realism of those digital components, compared to Fellowship.
Fellowship makes clever use of energetic cinematography and in-camera tricks for purposes both symbolic (Saruman constantly towering over Gandalf) and from a practical storytelling angle (Fellowship members tower over their Hobbit peers). It also has the benefit of grislier close-quarter combat sequences and brawls, but that is a stylistic choice (fitting with the darker tone of the Rings films in general); though, Fellowship is free of certain visual restrictions that An Unexpected Journey endures due to its use of 3D cameras and HFR format.
WINNER: Fellowship of the Ring for action, An Unexpected Journey for effects.
Overall, An Unexpected Journey has its flaws; although there's nary a scene that doesn't serve a purpose or lay groundwork for development in a later film, it does feel overstuffed. However, the direction is quite confident, editing is consistent and pacing shifts very consciously faster and slower. Everything from characterization to bridge-work for later films is conducted with an assured hand - even one prone to lavishing brushstrokes that sometimes come off as too-much.
Fellowship does not become 'weak' when juxtaposed with An Unexpected Journey; rather, Jackson's energy right out of the gate is observable in every facet of the former. However, there's a roughness that Hobbit doesn't suffer from, like choppy passages in terms of editing (see: Gandalf and Frodo traveling through the Shire). Similarly, there are character arcs with enough missing material, they seem to almost come from nowhere in the theatrical cut (see: Aragorn's commitment to Gondor, upon Boromir's death).
Bear in mind, Fellowship remains an amazing accomplishment; indeed, these complaints are the results of an eye scrutinizing the film very closely. Nonetheless, it was the first blockbuster under-taken by Jackson - with more experience on his side, his output has improved overall.
WINNER: An Unexpected Journey
And So, the Overall Winner Is...