Geromino: They are both healers, sometimes also called defensive spellcaster, but also two different classes and each have their own set of special features.
Pretty much like Rogue and Bard, who are both tricksters, but different.
Or Fighter, Barbarian, Paladin and Ranger, all of whom are different versions of the warrior.
Or Wizard, Sorcerer and Warlock, all of whom are variants of the wizard or mage or offensive spellcaster.
Clerics traditionally are more tanky and fighterlike. And yes they are very anti-undead, or sometimes pro-undead.
Druids have the whole nature theme going on, which means they get stronger offensive spells. And they get features like Wildshape.
Which you prefer is totally up to you. In BG1 and BG2 one always wanted one of each in group. With only four people in group, well, you are more likely to only have one now.
Thanks for the information.
Zaxares: Others have already covered the mechanical aspects of choosing between the two classes, so I'll focus my answer more from a RP perspective. :)
Druids are more concerned with the overall balance of nature, and of protecting a specific biome within their area of influence. The stereotypical Druid, for example, typically assumes stewardship over a particular forest, mountain, swamp etc. and takes steps to preserve it from those who would harm or destroy the existing equilibrium of the biome. (Often this refers to loggers, miners, farmers etc. but they can also come into conflict against other druidic circles at times. Druids (especially in the Forgotten Realms) can pay homage or venerate nature deities like Silvanus or Chauntea, but they do not worship them in the same way that clerics do. Their powers are derived from the bond with nature itself, not through the divine graces of a deity.
In contrast, Clerics have dedicated themselves to the worship and precepts of a particular deity and its church. Their goal is to spread and enforce their deity's will, regardless of how this might affect the balance of the natural world. While their actions may typically align with that of Druids, if Silvanus decided that, say, a hot spring in the middle of an arctic tundra was not appropriate, his clerics would have to obey his edicts to destroy that hot spring, even though a druid might object and point out that the animals of the arctic use that hot spring as a stopover point during their winter migrations and thus destroying it could drastically affect their populations.
That was really insightful, thank you.