Check out the Rogue's Handbook thread on the Wizards CharOp boards. It explains some of the better ways to get around at least a few of the initial class restrictions on rogues, all within RAW. The sheer volume of material posted in issues of Dragon, the Power books, and other sources change the nature of the game pretty extensively. Even if you don't twink out and over-optimize your character, you can still find some features that address the worst worries.

As for the skill system, it isn't as bad as you think. Remember that every skill gains a bonus of 1/2 your character level as you go up, and you can use a number of feats to boost those further (skill training feat for a skill outside your class list, skill focus for better talent in a trained skill, jack of all trades for a minor but wide-reaching boost...). Since the skill list is so small, and each skill is focused on those tasks related to the adventure you're likely to be having, you really don't have anyone who ends up being -useless- at skills.

As for the halfling issue...there's not much that can be said there. In 3e, it was the 'small weapons' rule, now it's one size of weapons all around and halflings just kind of have to make do. In practice it doesn't really cause problems for halfling rogues (for example), because many of the best rogue powers are dagger-based, as is the (arguably) most powerful Paragon Path, so...

tl;dr version (I do go on, don't I?)

Yes, the restrictions do feel cumbersome at first. However there are many options for getting around them as you grow, and being able to make a successful character who does so is really rewarding, and the edition is definitely worth your time to get to know.