Really, the main opponent I find myself arguing against time and again is reductionism. A main theme of my thesis was that an other, any subject or object (and for me the terms really are interchangeable), while wholly constituted of the material that composes it, should not be reduced to it; an entity, in order to be an entity rather than an aggregate, must admit of some kind of metaphysical unity.
It's also been an ongoing conviction that the truths of separate fields of investigation should not and cannot be reduced to each other; while I value science and scientific investigation immensely, I flinch whenever someone tries to explain religious claims in terms of a literal, "scientific" statement about the world(as you may imagine this happens often enough to constitute some kind of nervous tick; it is the error, in my opinion, of people both with and without religious conviction to claim that religious statements can hold the same kind of truth as scientific ones; that religion is principally an attempt at explaining or describing the world). Likewise I don't think biology should be reduced to chemistry or physics, or psychology to biology - or even sociology to psychology. And needless to say, art too has its own domain of value, truths of which are not explainable or even correctly stateable in terms of any other discipline.
I think a mistake that it's easy to make about this is in thinking that these separate domains or magisteria exist side-by-side; that this means religious truth, for example, is equal but complementary to scientific truth, because there is some "spiritual" realm sitting alongside the material. But this is to make the fundamental mistake of judging all meaning by the terms of materialism. There doesn't need to be a "real" realm in which religious truth happens in order for religious truth to be "real" in terms of having value and meaning. Just like psychological claims don't have to be stateable in terms of chemistry in order to be valid. There is a mental "realm" but it's not an objective one in the way we tend to think of the objectively real material world.
Perhaps my main complaint against reductionism is in the drive to totalise. When everything is stateable in a single tongue, according to a single model of reality, the world becomes static; the flat world of particles existing in mechanical relation according to a single overarching narrative or set of rules takes on, for me, a hellish aspect; a metaphysical fascism where value is already determined and even personal interpretation or sensation is not what it is but is only something else articulated into an apparent form. We end up with a cosmos which is nothing but numbers and the relationship between them. Reductionism aggressively roots out and throws away any alternative viewpoints, claiming that a single schema is the absolute truth, and all others are just articulations of the fundamental principle. This is highly unsatisfactory for me. It seems like a kind of death; an autopsy. (I've never been able to settle on just one thing; I can't even pick a favourite musical style, I need to listen to 'em all.) Worse yet a single system of value seems to negate even itself, because on what can that system of value, of meaning, actually ground itself? What gives the ultimate ground of reality its ultimate status? The question is like asking "who made God" or "what came before the Big Bang" I know, and perhaps it demonstrates the same basic misunderstanding of ultimacy (or of "reality"!). But I find the picture of separate realms interlinking and supporting each other much more intellectually pleasing; the idea that different (and even unrelated) systems of understanding the world-we-live-in allows for much greater depth of understanding and a much richer sense of the world; and the world-we-live-in after all isn't the objective material world of science, but a world infused with social, mythical, artistic and religious aspects, none of which exist in the material world which empirical science investigates.
Another aspect of this is in the field of comparative religion. It's been fashionable for a while to say that all religions are the same, that they all teach the same thing or that they're all paths to the same truth. I find this deeply unsatisfactory. What fascinating about religion is just how different they all are. The metaphysics, the soteriology and the system of value and meaning for human life are completely different in, say, Buddhism and Islam. Even in two religions which have deeply influenced each other throughout their history, like Judaism and Christianity, their understanding what it means to be human and how the human relates to the world and to the sphere of divinity (as well as to other humans) is really totally different (this is one of the reasons why Jewish philosophy is so different from typical post-Christian western philosophy). For me, Judaism fascinates me - but I wouldn't claim it's the only or best way of doing religion. I value equally (well, maybe not equally...) the teachings of all religions; these are human endeavours, constructed by humans to answer the specific questions which a group of people faced at a particular time, and subject to an evolutionary trajectory constrained by both the strictures of the initial dogma and the events which subsequent generations endured, altering their interpretations and emphases. Of course, reigions havealways existed in proximity to each other and many have absorbed concepts and traditions from other faiths; the boundaries are always permeable.
But further I think ther must be a means of escaping. No? When one system, one order, becomes too much one needs the possibility of escaping into another; of stepping out of the existing symbolic order and experiencing the world anew, through another. To realise that things don't have to be the way they seem; that redemption can come in various forms, from unexpected places; that the world can actually be turned upside down and reform into new shapes, with new relationships between its parts.