a few general thoughts....
I think that it is important to remember that incorporation was not something which came about immediately upon the ratification of the 14th, nor is there significant evidence in the congressional record to suggest that those who drafted it envisioned it being interpreted to allow for, or even require, incorporation. I think discussion of the 14th Amendment must be grounded in two things. First is an understanding of Reconstruction politics, and second (in the context of the first), is an understanding of American federalism.
It has been suggested by some scholars of federalism that the 14th Amendment essentially transformed the United States from a federal to a quasi-unitary system of government through the doctrine of incorporation. I would agree that this has been the result, but I do not believe that it was the intent. For the intent, I would refer you to Herman Belz, who has suggested that the 14th Amendment was primarily intended to repeal those provisions of the original Constitution which supported slavery. It simply ensured that the freed slaves enjoyed the same rights under the federal Constitution which whites had always been entitled to, while leaving the state-federal relationship unchanged. Records of the congressional debates support this view fairly well, I believe.
As to the question of how we can be said to have any constitutionally protected rights if they are not protected from both the state and federal governments, this brings us to my second point on the nature of American federalism. At the time of the adoption of the Bill of Rights, it was fairly well understood that it applied only to the federal government. Evidence of this can be found in the fact (for example) that states were not forced to comply with the 1st Amendment's establishment clause. Official state religions were considered to be state matters. Although all of the states finally did get rid of their official religions, they were not forced to do so under the 1st Amendment. The American federal system, as originally established, permitted the states to manage their own internal affairs almost completely and left the protection of rights at the state level to the people of the states to ensure through their own constitutional arrangements. Incorporation is clearly inconsistent with this idea. It instead imposes what has essentially become federal "baseline" rights which must be applied to the state governments since they are considered to be fundamental and necessary to the concept of ordered liberty.
I believe that there are several problems with this idea. First, it is the manifestation of Madison's fear that in enumerating specific rights we would give the false impression that the enumerated rights were somehow more important than other, unenumerated rights, and that the enumeration was necessary in order to protect them from infringement by the government. This is one of the reasons why Madison initially opposed the addition of a Bill of Rights to the Constitution, and provides the necessary context for understanding the 9th and 10th Amendments.
Second, incorporation is almost entirely subjective and truly does lead us to an inevitable situation of judicial activism and supremacy. Who decides which rights are fundamental, and therefore should be incorporated? What objective criteria are used in making the determination? How can a right be fundamental according to one Court, and found not to be by a succeeding one? Incorporation muddies the constitutional waters by blurring the separation of powers both between the judicial branch and the legislative branch and between the states and the federal government.
Finally, incorporation invites (even greater) political partisanship into constitutional issues. Rather than delineating the boundaries between state and federal authority, incorporation allows the judicial branch to involve itself in what are essentially political matters. The Heller decision and the broader debate over the 2nd Amendment provide a perfect current example. It seems likely to me that the Court will incorporate the 2nd Amendment. While the outcome may be one that I would support, the means of achieving it is not only constitutionally shaky, but also completely unnecessary. We need not find that the individual right to keep and bear arms (as affirmed in Heller) is a fundamental right which must be incorporated in order to preserve it. All that is required is a return to the pre-incorporation understanding of American federalism. That would necessitate the conclusion that federal firearms restrictions are, for the most part, unconstitutional and that the state legislatures are the proper place to fight the battle over gun rights within the states. For those states which have constitutional language which is substantially similar to the 2nd Amendment, we can assume that the state courts would come to a conclusion similar to that which the Supreme Court reached. For those states which do not, the issue, like so many which have been essentially removed from the states' sphere, would be properly fought out within the states. As a conservative, it is likely that I would not like the outcome in some states. However, the imposition of federal rights upon the states should be viewed suspiciously no matter whether they seem to be favorable to liberals or conservatives. On the opposite side of the spectrum, I would make exactly the same argument regarding same-sex marriage. The specific issue is irrelevant. It is the basic constitutional principles which are important.