Segueを使ってUINavigationControllerの画面遷移アニメーションを変更する ref: http://qiita.com/roothybrid7/items/532b63175da30fa9a2b1

MasterViewController.m

#import "MasterViewController.h"

#import "DetailViewController.h"
#import "MyNavigationController.h"
#import "NavigateFlipSegue.h"

@interface MasterViewController () <MyNavigationControllerDelegate> // 委譲用プロトコルの適用
- (void)configureCell:(UITableViewCell *)cell atIndexPath:(NSIndexPath *)indexPath;
@end

@implementation MasterViewController

- (void)prepareForSegue:(UIStoryboardSegue *)segue sender:(id)sender
{
    if ([[segue identifier] isEqualToString:@"showDetail"]) {
        NSIndexPath *indexPath = [self.tableView indexPathForSelectedRow];
        NSManagedObject *object = [[self fetchedResultsController] objectAtIndexPath:indexPath];
        [[segue destinationViewController] setDetailItem:object];
    }
}

// unwind segueの定義
- (IBAction)exitToMasterView:(UIStoryboardSegue *)segue
{
    // XXX: No-op. unwind segue.
}

#pragma mark - MyNavigationControllerDelegate

// 委譲用プロトコルメソッドの実装
- (UIStoryboardSegue *)segueInNavigationControllerForUnwindingToViewController:(UIViewController *)toViewController fromViewController:(UIViewController *)fromViewController identifier:(NSString *)identifier
{
    if ([identifier isEqualToString:@"existFromDetail"]) {  // custom segueの生成
        NavigateFlipSegue *segue = [[NavigateFlipSegue alloc] initWithIdentifier:identifier source:fromViewController destination:toViewController];
        segue.unwind = YES; // unwind segueなのでセット
        return segue;
    }
    return nil;
}

MyNavigationController.h

#import <UIKit/UIKit.h>

// ChildViewControllerで実装
@protocol MyNavigationControllerDelegate <NSObject>

/*!
    @method segueInNavigationControllerForUnwindingToViewController:fromViewController:identifier:
    @abstract NavigationControllerによる遷移でunwindする場合、custom segueを使いたい場合に実装する
    @discussion 戻る側のViewControllerでunwind segueの実装してNavigationControllerでは何もしない(委譲)
    @return Custom Segueを生成して返すように実装
 */
- (UIStoryboardSegue *)segueInNavigationControllerForUnwindingToViewController:(UIViewController *)toViewController fromViewController:(UIViewController *)fromViewController identifier:(NSString *)identifier;

@end

@interface MyNavigationController : UINavigationController

@end

MyNavigationController.m

#import "MyNavigationController.h"

@interface MyNavigationController ()

@end

@implementation MyNavigationController

- (UIStoryboardSegue *)segueForUnwindingToViewController:(UIViewController *)toViewController fromViewController:(UIViewController *)fromViewController identifier:(NSString *)identifier
{
    // MARK: 実際の戻り先ChildViewControllerに処理を任せる
    if ([toViewController conformsToProtocol:@protocol(MyNavigationControllerDelegate)]) {
        id <MyNavigationControllerDelegate> destinationViewController = (id <MyNavigationControllerDelegate>)toViewController;
        UIStoryboardSegue *segue = [destinationViewController segueInNavigationControllerForUnwindingToViewController:toViewController fromViewController:fromViewController identifier:identifier];
        if (segue) {
            return segue;
        }
    }

    return [super segueForUnwindingToViewController:toViewController fromViewController:fromViewController identifier:identifier];
}

@end

NavigateFlipSegue.h

#import <UIKit/UIKit.h>

@interface NavigateFlipSegue : UIStoryboardSegue

@property (nonatomic) BOOL unwind;  // unwind segueのインスタンスを作成時に設定するflag

@end

NavigateFlipSegue.m

#import "NavigateFlipSegue.h"

@implementation NavigateFlipSegue

- (void)perform
{
    UIViewController *sourceViewController = self.sourceViewController;
    UIViewController *destinationViewController = self.destinationViewController;
    UINavigationController *navigationController = sourceViewController.navigationController;

    if (self.unwind) {  // Unwind segueの場合は、右からflipするアニメーション
        [UIView transitionWithView:navigationController.view duration:0.3f options:UIViewAnimationOptionTransitionFlipFromRight animations:^{
            [navigationController popToRootViewControllerAnimated:NO];
        } completion:nil];
    } else {    // segueの場合は、左からflipするアニメーション
        [UIView transitionWithView:navigationController.view duration:0.3f options:UIViewAnimationOptionTransitionFlipFromLeft animations:^{
            [navigationController pushViewController:destinationViewController animated:NO];
        } completion:nil];
    }
}