The book itself tends to be rather schizophrenic, and for good reason. Le Morte d'Arthur is actually a collection of many other Arthurian legends, some of which had existed for hundreds of years before Malory decided to record them in his opus. In addition, the book was only published posthumously and the printer, William Caxton, did a rather clumsy job editing the text. This has lead to some mechanical issues which can make the text rather difficult to read and it has a tendency to reiterate points already made before. The best way to approach this book is to treat it as an anthology that spans hundreds of years of European history.
The biggest challenge I had with this book, and this is an issue I've had with other works like The Aeneid and The Illiad where it tends to contain a lot of very repetitive fighting. People proffer to joust and then strike many sad strokes and smite on the left hand and on the right hand and win much worship. I understand that these rather repetitive elements exist so that bards and troubadours could easily remember these stories when they were telling them to nobility, but it becomes very tedious to read as a twenty-first century audience. The largest portion of this book, the story of Sir Tristan, has a significant amount of such fighting and became a forced march at some points. Again, this is really a product of the story being hundreds of years old, but it makes it very difficult for a twenty-first century reader anyway.
The other thing that really surprised me was the fact that there was a great level of corruption within Arthur's court from the very beginning, which ultimately leads to the fall of the Round Table. Many of you are probably aware of the adulterous relationship between Sir Lancelot and Queen Guinevere, but that is not the only disreputable act committed by men who are, ostensibly, the flower of knightly chivalry. Sir Gawain and his brothers, for example, murder Sir Lamorak over a blood feud and numerous other petty quarrels seem to constantly strain the peace of Arthur's realm. Perhaps what was most surprising to me was the fact that Arthur willingly had sex with his sister, Morgan la Fey, thus conceiving his son and nephew Sir Mordred. In most of the versions I had read previously, which were the type cleaned up to make them appropriate for young boys, Morgan la Fey is portrayed as enchanting or deceiving Arthur because she's evilly plotting the downfall of Arthur's reign, almost as soon as it begins. Really, despite the glory and chivalry of Arthur's knights it seems like Camelot was doomed from the very beginning because of the sins that rotted it from the inside out.
Some portions of this book I think modern audiences could still really enjoy. I know I enjoyed the story of Sir Gareth and the portion dedicated to the quest for the Holy Grail, but other portions like Arthur's war with the Emperor Lucius and the tale of Sir Tristan drag because of their repetitive nature. I would recommend on the whole though, that only the serious Arthur scholar read the whole of Le Morte d'Arthur. I think the more casual fans would be better served by reading many of the excellent adaptations which have come along in the intervening five centuries.