The prevalent opinion of SC2 players is that SC2 is a step forward in game mechanics and gameplay. However SC2 has major drawbacks that prevent it from dethroning the original game.
SC2 Engine Flaws:
1.SC2 is tied to blizzard servers: All games, map uploads, tournaments, are controlled and limited by Blizzard. SC has unlimited "map uploads" since its games hosted by players and private servers only serve as lobby/channel.
2.SC2 doesn't have low-latency games because it lacks LAN/IP networking: it simply incapable of being in the same league of performance as SC(and the hefty 3D engine doesn't help).
3.SC2 engine has major performance demands and uses much more of memory/CPU.
Many players use integrated and old GPUs, which are incapable of any settings beside lowest(if the game loads at all).
4.SC2 takes enormous space (~30GB for basic) and its updates/patches are huge.
The game is filled with tons of art assets and single-player contents.(a version without the music/sounds/cinematics/single-player campaigns would be really great for players with small SSD or those with little space to spare).
5.SC2 editor is needlessly complex and prone to crashing: it also a memory hog for anything but simplest maps, and all maps are stored on blizzard servers. SC has numerous third party editors, none tied to any servers. Maps are much larger and take longer to download. You can't test/update maps quickly as in starcraft(i could rewrite map versions between games: alt-tab, edit a fix,save as new versions,host new game ).
More on maps:
6.SC2 is both too complex and too wasteful of screen real-estate: Broodwar present all options in sane manner and dedicates most space to the game/chat window. UI design of SC2 is best described as "military eyecandy" will useless symbols, emblems and filler graphical elements taking up the most space.

SC2 Gameplay Flaws:
1.The game is filled with overpowered units that have to be hard-countered exactly:
BW system of soft-counters is more flexible and allows skilled players to win with inferior units.
2.Game mechanics are modified towards less skill: the player involvement is simplified to reduce micromanagement and focus on economy. Now there is some misunderstanding: the 12 Unit limit removal is not the key difference,
3.SC2 units are simply more powerful, more ranged and hard-hitting so having any of them in a "deathball" (a group of ranged units) negates all range vs melee balance mechanics. There is tendency to have unbalanced mary-sue "uber-units" produced en-masse, vs Broodwar unit design where each unit had flaws(damage type, speed, range,armor) and weakness(soft-counters).
In SC2 the "weakness" is that there is a hard-counter unit that needs to be massed exactly opposite the enemy composition. Upgrades in SC2 even negate the unit flaws and make them resistant to counters.
4. Balance of the races: despite constant patches, expansions and newer maps. SC2 is not balanced to the degree of being stable(even vs pre1.08 broodwar).
The amount of units and their stats make it much harder than broodwar's limited unit choice. The result is that at any point there is a race with some advantage not countered by anything else and requiring a patch fix(which invariably breaks something else or uncovers another advantage/glitch).
Players has to relearn the game and adjust to new balance every patch:Broodwar doesn't mess with well-established build orders and counters.
5.SC2 is more of a economic competition. In Broodwar micro control is crucial: AI is much dumber in Broodwar and those ignoring their units lose them fast: the "default state" AI of idle units allows them to be sniped or lured easily(it also allows awesome tricks).